Super-enhancers and methods of use thereof

ABSTRACT

The present invention relates in some aspects to super-enhancers and related compositions, methods, and agents that are useful for modulating expression of cell type-specific genes that are required for maintenance of cell identity (e.g., embryonic stem cell identity) or maintenance of a disease state (e.g., cancer).

RELATED APPLICATIONS

This application is a continuation-in-part of U.S. patent application Ser. No. 14/523,560, filed Oct. 24, 2014, which is a continuation of U.S. application Ser. No. 14/063,337, filed on Oct. 25, 2013, which claims benefit of U.S. Provisional Application Nos. 61/718,697, filed Oct. 25, 2012, and 61/799,646, filed Mar. 15, 2013. This application is also a continuation of U.S. patent application Ser. No. 14/063,894, filed Oct. 25, 2013, which claims benefit of U.S. Provisional Application Nos. 61/718,697, filed Oct. 25, 2012, 61/799,646, filed Mar. 15, 2013, and 61/889,302, filed Oct. 10, 2013. The entire teachings of the above applications are incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with government support under RO1-HG002668, RO1-CA146445, and RO1-CA109901, awarded by the National Institutes of Health. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Regulatory elements (e.g., transcription factors, cis-acting enhancer elements, transcriptional coactivators and chromatin regulators) activate gene expression programs in cells ranging from embryonic stem cells (ESCs) to tumor cells. Regulatory elements are important for maintenance of cell identity (e.g., ESC identity) and of some disease states (e.g., cancer). The mechanisms underlying how regulatory elements contribute to maintenance of cell identity and of disease state are not entirely understood.

SUMMARY OF THE INVENTION

The present invention relates in some aspects to super-enhancers and related compositions, methods, and agents that are useful for modulating expression of cell type-specific genes that are required for maintenance of cell identity (e.g., embryonic stem cell identity) or maintenance of a disease state (e.g., cancer, Alzheimer's disease, Type 1 diabetes, and systemic lupus erythematosus).

In some aspects, the invention provides an isolated super-enhancer, or functional fragment and/or variant thereof, comprising a genomic region of deoxyribonucleic acid (DNA) that contains at least two enhancers, wherein the genomic region is occupied when present within a cell by more, e.g., 2, 3, 4, 5, 10, or 15 fold more super-enhancer component, e.g., an eRNA or a chromatin associated protein, e.g., a transcriptional coactivator, than the average single enhancer within the cell.

A super-enhancer component, as used herein, is a component, such as a protein, that has a higher local concentration, or exhibits a higher occupancy, at a super-enhancer, as opposed to a normal enhancer or an enhancer outside a super-enhancer, and in embodiments, contributes to increased expression of the associated gene. In an embodiment, the super-enhancer component is a nucleic acid (e.g., RNA, e.g., eRNA transcribed from the super-enhancer, i.e., an eRNA). In an embodiment, the nucleic acid is not chromosomal nucleic acid. In an embodiment, the component is involved in the activation or regulation of transcription.

In an embodiment, the super-enhancer is a super-enhancer described herein, e.g., in any of Tables 1-90. Tables 5-90 are provided as an Appendix to the subject Specification and are fully incorporated herein by reference.

In an embodiment, the super-enhancer comprises a genetic signature, e.g., a genetic signature associated with the presence or absence of a disease state.

In some embodiments, the super-enhancer component comprises RNA polymerase II, Mediator, cohesin, Nipb1, p300, CBP, Chd7, Brd4, and components of the esBAF (Brg1) or a Lsd1-Nurd complex (e.g., RNA polymerase II).

In an embodiment the super-enhancer comprises all or part of a gene under its control. In an embodiment does not contain a complete associated gene.

In an embodiment, the gene is comprises a disease-associated variation such as a SNP. In an embodiment, the gene is an oncogene or a gene having a function associated with a cancer hallmark.

In some embodiments the transcriptional coactivator is Mediator. In some embodiments the transcriptional coactivator is Med1.

In some embodiments the genomic region is occupied when present within a cell by more super-enhancer component, e.g., more chromatin regulator or more RNA such as eRNA, than the average single or normal enhancer within the cell.

In some embodiments the chromatin regulator is a BET bromodomain protein. In some embodiments the BET bromodomain protein is BRD4.

In some embodiments the genomic region spans between about 4 kilobases and about 500 kilobases in length. In some embodiments the genomic region spans between about 4 kilobases and about 40 kilobases in length.

In some embodiments the genomic region spans sufficient nucleic acid, or the super-enhancer is of sufficient size or structure, such that, when associated with a gene, the gene has substantially greater expression than in the absence of the super-enhancer. In an embodiment, the gene expression is at least 1.5 times greater (e.g., at least 2, at least 3, at least 4, at least 5 or at least 10 times greater) than the gene expression in the absence of the super-enhancer.

In some embodiments the at least two enhancers are clustered together.

In some embodiments each enhancer comprises a binding site for a cognate transcription factor.

In some embodiments the cognate transcription factor comprises an embryonic stem cell master transcription factor. In some embodiments the embryonic stem cell master transcription factor is one or more of Oct4, Sox2, Nanog, Esrrb, Utf1, Klf4, mir-290-295 microRNA gene cluster, Tbx3, or Sgk1. In some embodiments, the embryonic stem cell master transcription factor is one or more of Nr5a2, Prdm14, Tcfcp211, Smad3, Stat3 or Tcf3. In some embodiments, the embryonic stem cell master transcription factor Oct 4, Sox2, Nanog, Klf4, Esrrb, Nr5a2, Prdm14, Tcfcp211, Smad3, Stat3 or Tcf3. In some embodiments, the transcription factor is directly down to its known DNA sequence motif.

In some embodiments a super-enhancer component comprises an enzyme that, adds, detects or reads, or removes a functional group, e.g., a methyl or acetyl group, from a chromatin component, e.g., DNA or histones.

In some embodiments a super-enhancer component comprises an enzyme that alters, reads, or detects the structure of a chromatin component, e.g., DNA or histones, e.g., a DNA methylase or demethylase, a histone methylase or demethylase, or a histone acetylase or de-acetylase that write, read or erase histone marks, e.g., H3K4me1 or H3K27Ac.

In some embodiments a super-enhancer component comprises an enzyme that adds, detects or reads, or removes a functional group, e.g., a methyl or acetyl group, from a chromatin component, e.g., DNA or histones.

In some embodiments the super-enhancer component comprises a protein needed for development into, or maintenance of, a selected cellular state or property, e.g., a state of differentiation, development or disease, e.g., a cancerous state, or the propensity to proliferate or the propensity or the propensity to undergo apoptosis. In some embodiments the disease state is a proliferative disease, an inflammatory disease, a cardiovascular disease, a neurological disease or an infectious disease.

In some embodiments the cognate transcription factor comprises an oncogenic transcription factors. In some embodiments the oncogenic transcription factor is selected from the group consisting of c-Myc, IRF4, p53, AP-1, Bcr-Abl, c-Fos, c-Jun and combinations thereof. In some embodiments the cognate transcription factor comprises a muscle cell transcription factor. In some embodiments the transcription factor is MyoD.

In some embodiments the cognate transcription factor comprises a B cell transcription factor. In some embodiments the transcription factor is Pu.1.

In some embodiments, the cognate transcription factor comprises a transcription factor of a gene associated with a hallmark of a disease such as cancer. In some embodiments, the cognate transcription factor comprises a transcription factor of a gene having a disease associated DNA sequence variation such as a SNP. In some embodiments, the disease is Alzheimer's disease, and the gene is BIN1 (e.g., having a disease associated DNA sequence variation such as a SNP). In some embodiments, the disease is type 1 diabetes, and the gene is associated with a primary Th cell (e.g., having a disease associated DNA sequence variation such as a SNP). In some embodiments, the disease is systemic lupus erythematosus, and the gene plays a key role in B cell biology (e.g., having a disease associated DNA sequence variation such as a SNP).

In some embodiments, the gene comprises a disease-associated variation related to rheumatoid arthritis, multiple sclerosis, systemic scleroderma, primary biliary cirrhosis, Crohn's disease, Graves disease, vitiligo and atrial fibrillation. In some embodiments, a cognate transcription factor is associated with a healthy or diseased cell or tissue, e.g., in one or more of the following cells or tissues. In some embodiments the cell is a mammalian cell. In some embodiments the cell is a human cell. In some embodiments the cell is an embryonic stem cell or embryonic stem cell-like cell. In some embodiments the cell is a muscle cell. In some embodiments the muscle cell is a myotube. In some embodiments the cell is a B cell. In some embodiments the B cell is a Pro-B cell.

In some embodiments the cell is from the brain. In some embodiments the cell is an astrocyte cell. In some embodiments the cell is from the angular gyms of the brain. In some embodiments the cell is from the anterior caudate of the brain. In some embodiments the cell is from the cingulate gyms of the brain. In some embodiments the cell is from the hippocampus of the brain. In some embodiments the cell is from the inferior temporal lobe of the brain. In some embodiments the cell is from the middle frontal lobe of the brain.

In some embodiments the cell is a naïve T cell. In some embodiments the cell is a memory T cell. In some embodiments the cell is CD4 positive. In some embodiments the cell is CD25 positive. In some embodiments the cell is CD45RA positive. In some embodiments the cell is CD45RO positive. In some embodiments the cell is IL-17 positive. In some embodiments the cell is stimulated with PMA. In some embodiments the cell is a Th cell. In some embodiments the cell is a Th17 cell. In some embodiments the cell is CD255 positive. In some embodiments the cell is CD127 positive. In some embodiments the cell is CD8 positive. In some embodiments the cell is CD34 positive.

In some embodiments the cell is from the duodenum. In some embodiments the cell is from smooth muscle tissue of the duodenum.

In some embodiments the cell is from skeletal muscle tissue. In some embodiments the cell is a myoblast cell. In some embodiments the cell is a myotube cell.

In some embodiments the cell is from the stomach. In some embodiments the cell is from smooth muscle tissue of the stomach.

In some embodiments the cell is CD3 positive. In some embodiments the cell is CD8 positive. In some embodiments the cell is CD14 positive. In some embodiments the cell is CD19 positive. In some embodiments the cell is CD20 positive. In some embodiments the cell is CD34 positive. In some embodiments the cell is CD56 positive.

In some embodiments the cell is from the colon. In some embodiments the cell is a crypt cell. In some embodiments the cell is a colon crypt cell.

In some embodiments the cell is from the intestine. In some embodiments the cell is from the large intestine. In some embodiments the intestine is from a fetus. In some embodiments the cell is a DND41 cell. In some embodiments the cell is a GM12878 cell. In some embodiments the cell is a H1 cell. In some embodiments the cell is a H2171 cell. In some embodiments the cell is a HCC1954 cell. In some embodiments the cell is a HCT-116 cell. In some embodiments the cell is a HeLa cell. In some embodiments the cell is a HepG2 cell. In some embodiments the cell is a HMEC cell. In some embodiments the cell is a HSMM tube cell. In some embodiments the cell is a HUVEC cell. In some embodiments the cell is a IMR90 cell. In some embodiments the cell is a Jurkat cell. In some embodiments the cell is a K562 cell. In some embodiments the cell is a LNCaP cell. In some embodiments the cell is a MCF-7 cell. In some embodiments the cell is a MM1S cell. In some embodiments the cell is a NHLF cell. In some embodiments the cell is a NHDF-Ad cell. In some embodiments the cell is a RPMI-8402 cell. In some embodiments the cell is a U87 cell.

In some embodiments the cell is an osteoblast cell. In some embodiments the cell is from the pancreas. In some embodiments the cell is from a pancreatic cancer cell.

In some embodiments the cell is from adipose tissue. In some embodiments the cell is from the adrenal gland. In some embodiments the cell is from the bladder. In some embodiments the cell is from the esophagus. In some embodiments the cell is from the stomach. In some embodiments the cell is a gastric cell. In some embodiments the cell is from the left ventricle. In some embodiments the cell is from the lung. In some embodiments the cell is from a lung cancer cell. In some embodiments the cell is a fibroblast cell.

In some embodiments the cell is from the ovary. In some embodiments the cell is from the psoas muscle. In some embodiments the cell is from the right atrium. In some embodiments the cell is from the right ventricle. In some embodiments the cell is from the sigmoid colon. In some embodiments the cell is from the small intestine. In some embodiments the cell is from the spleen. In some embodiments the cell is from the thymus.

In some embodiments the cell is a VACO 9M cell. In some embodiments the cell is a VACO 400 cell. In some embodiments the cell is a VACO 503 cell.

In some embodiments the cell is from the aorta.

In some embodiments the cell is from the brain. In some embodiments the cell is a brain cancer cell.

In some embodiments the cell is from the breast. In some embodiments the cell is a breast cancer cell.

In some embodiments the cell is from the cervix. In some embodiments the cell is a cervical cancer cell.

In some embodiments the cell is from the colon. In some embodiments the cell is from a colorectal cancer cell.

In some embodiments the cell is a blood cell. In some embodiments the blood cell is a monocyte cell. In some embodiments the blood cell is a B cell. In some embodiments the blood cell is a T cell. In some embodiments the blood cell is a human embryonic stem cell. In some embodiments the blood cell is a cancerous blood cell. In some embodiments the blood cell is from a fetus.

In some embodiments the cell is from bone. In some embodiments the bone cell is an osteoblast cell.

In some embodiments the cell is from the heart. In some embodiments the cell is a mammary epithelial cell. In some embodiments the cell is a skin cell. In some embodiments the skin cell is a fibroblast cell.

In some embodiments the cell is an embryonic stem cell. In some embodiments the cell is from the umbilical vein. In some embodiments the cell from the umbilical vein is an endothelial cell.

In some embodiments the cell is from the colon. In some embodiments the cell is from the prostate. In some embodiments the cell is a prostate cancer cell.

In some embodiments the cell is from the liver. In some embodiments the cell is a liver cancer cell.

In some embodiments the cell is from the muscle. In some embodiments the muscle is from a fetus.

In some embodiments the cell is from the thymus. In some embodiments the thymus is from a fetus. In some embodiments the genomic region is occupied when present within the cell by an order of magnitude more super-enhancer component, e.g., transcriptional coactivator than the average single enhancer within the cell. In some embodiments the order of magnitude is at least about 2-fold. In some embodiments the order of magnitude is at least about 10-fold. In some embodiments the order of magnitude is at least about 15-fold. In some embodiments the order of magnitude is at least about 16-fold.

In some aspects, the invention provides a composition comprising a super-enhancer of the present invention.

In some aspects, the invention provides a nucleic acid construct comprising a super-enhancer, or functional fragment and/or variant thereof, of the present invention. In some embodiments the nucleic acid construct includes a nucleotide sequence encoding a target gene operatively linked to the super-enhancer. In some embodiments the nucleic acid construct includes a reporter construct.

In some aspects, the invention provides a cell transfected with a nucleic acid construct comprising a super-enhancer, or functional fragment and/or variant thereof, operatively linked to a target gene wherein upon transfection of the cell with the nucleic acid construct endogenous transcriptional coactivators and chromatin regulators within the cell co-occupy the enhancers and the active transcription start sites of the target gene to stimulate high levels of expression of the target gene within the cell. In some embodiments, the enhancer is further occupied by RNA, e.g., eRNA.

In some embodiments the cell is a mammalian cell. In some embodiments the cell is a human cell. In some embodiments the cell is an embryonic stem cell or embryonic stem cell-like cell. In some embodiments the cell is a muscle cell. In some embodiments the muscle cell is a myotube. In some embodiments the cell is a B cell. In some embodiments the B cell is a Pro-B cell.

In some embodiments the cell is from the brain. In some embodiments the cell is an astrocyte cell. In some embodiments the cell is from the angular gyms of the brain. In some embodiments the cell is from the anterior caudate of the brain. In some embodiments the cell is from the cingulate gyms of the brain. In some embodiments the cell is from the hippocampus of the brain. In some embodiments the cell is from the inferior temporal lobe of the brain. In some embodiments the cell is from the middle frontal lobe of the brain.

In some embodiments the cell is a naïve T cell. In some embodiments the cell is a memory T cell. In some embodiments the cell is CD4 positive. In some embodiments the cell is CD25 positive. In some embodiments the cell is CD45RA positive. In some embodiments the cell is CD45RO positive. In some embodiments the cell is IL-17 positive. In some embodiments the cell is stimulated with PMA. In some embodiments the cell is a Th cell. In some embodiments the cell is a Th17 cell. In some embodiments the cell is CD255 positive. In some embodiments the cell is CD127 positive. In some embodiments the cell is CD8 positive. In some embodiments the cell is CD34 positive.

In some embodiments the cell is from the duodenum. In some embodiments the cell is from smooth muscle tissue of the duodenum.

In some embodiments the cell is from skeletal muscle tissue. In some embodiments the cell is a myoblast cell. In some embodiments the cell is a myotube cell.

In some embodiments the cell is from the stomach. In some embodiments the cell is from smooth muscle tissue of the stomach.

In some embodiments the cell is CD3 positive. In some embodiments the cell is CD8 positive. In some embodiments the cell is CD14 positive. In some embodiments the cell is CD19 positive. In some embodiments the cell is CD20 positive. In some embodiments the cell is CD34 positive. In some embodiments the cell is CD56 positive.

In some embodiments the cell is from the colon. In some embodiments the cell is a crypt cell. In some embodiments the cell is a colon crypt cell.

In some embodiments the cell is from the intestine. In some embodiments the cell is from the large intestine. In some embodiments the intestine is from a fetus.

In some embodiments the cell is a DND41 cell. In some embodiments the cell is a GM12878 cell. In some embodiments the cell is a H1 cell. In some embodiments the cell is a H2171 cell. In some embodiments the cell is a HCC1954 cell. In some embodiments the cell is a HCT-116 cell. In some embodiments the cell is a HeLa cell. In some embodiments the cell is a HepG2 cell. In some embodiments the cell is a HMEC cell. In some embodiments the cell is a HSMM tube cell. In some embodiments the cell is a HUVEC cell. In some embodiments the cell is a IMR90 cell. In some embodiments the cell is a Jurkat cell. In some embodiments the cell is a K562 cell. In some embodiments the cell is a LNCaP cell. In some embodiments the cell is a MCF-7 cell. In some embodiments the cell is a MM1 S cell. In some embodiments the cell is a NHLF cell. In some embodiments the cell is a NHDF-Ad cell. In some embodiments the cell is a RPMI-8402 cell. In some embodiments the cell is a U87 cell.

In some embodiments the cell is an osteoblast cell. In some embodiments the cell is from the pancreas. In some embodiments the cell is from a pancreatic cancer cell.

In some embodiments the cell is from adipose tissue. In some embodiments the cell is from the adrenal gland. In some embodiments the cell is from the bladder. In some embodiments the cell is from the esophagus. In some embodiments the cell is from the stomach. In some embodiments the cell is a gastric cell. In some embodiments the cell is from the left ventricle. In some embodiments the cell is from the lung. In some embodiments the cell is from a lung cancer cell. In some embodiments the cell is a fibroblast cell.

In some embodiments the cell is from the ovary. In some embodiments the cell is from the psoas muscle. In some embodiments the cell is from the right atrium. In some embodiments the cell is from the right ventricle. In some embodiments the cell is from the sigmoid colon. In some embodiments the cell is from the small intestine. In some embodiments the cell is from the spleen. In some embodiments the cell is from the thymus.

In some embodiments the cell is a VACO 9M cell. In some embodiments the cell is a VACO 400 cell. In some embodiments the cell is a VACO 503 cell.

In some embodiments the cell is from the aorta.

In some embodiments the cell is from the brain. In some embodiments the cell is a brain cancer cell.

In some embodiments the cell is from the breast. In some embodiments the cell is a breast cancer cell.

In some embodiments the cell is from the cervix. In some embodiments the cell is a cervical cancer cell.

In some embodiments the cell is from the colon. In some embodiments the cell is from a colorectal cancer cell.

In some embodiments the cell is a blood cell. In some embodiments the blood cell is a monocyte cell. In some embodiments the blood cell is a B cell. In some embodiments the blood cell is a T cell. In some embodiments the blood cell is a human embryonic stem cell. In some embodiments the blood cell is a cancerous blood cell. In some embodiments the blood cell is from a fetus.

In some embodiments the cell is from bone. In some embodiments the bone cell is an osteoblast cell.

In some embodiments the cell is from the heart. In some embodiments the cell is a mammary epithelial cell. In some embodiments the cell is a skin cell. In some embodiments the skin cell is a fibroblast cell.

In some embodiments the cell is an embryonic stem cell. In some embodiments the cell is from the umbilical vein. In some embodiments the cell from the umbilical vein is an endothelial cell.

In some embodiments the cell is from the colon. In some embodiments the cell is from the prostate. In some embodiments the cell is a prostate cancer cell.

In some embodiments the cell is from the liver. In some embodiments the cell is a liver cancer cell.

In some embodiments the cell is from the muscle. In some embodiments the muscle is from a fetus.

In some embodiments the cell is from the thymus. In some embodiments the thymus is from a fetus.

In some aspects, the invention provides a method of increasing the level of expression of a target gene in a cell, comprising transfecting a cell under conditions suitable for expression of the target gene with a nucleic acid expression construct comprising a nucleic acid sequence encoding the target gene operatively linked to a super enhancer, or functional fragment and/or variant thereof, wherein upon transfection of the cell endogenous transcriptional coactivators and chromatin regulators within the cell co-occupy enhancers clustered within the super enhancer, or functional fragment and/or variant thereof, and active transcription start sites of the target gene to increase the level of expression of the target gene within the cell. In some embodiments the level of expression of the target gene is increased 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, or more within the cell. In some embodiments, the enhancer is further occupied by RNA, e.g., eRNA.

In some aspects the invention provides a kit for increasing the expression of a target gene in a cell, comprising: (a) a nucleic acid construct comprising an artificial super-enhancer, or functional fragment and/or variant thereof, operatively linked to the target gene; (b) a population of cells suitable for expression of said target gene; and (c) a reagent for transfecting said population of cells with said nucleic acid construct.

In some aspects the invention provides a method of identifying a super enhancer, or functional fragment and/or variant thereof, in a cell, comprising: (a) identifying a genomic region of DNA within said cell characterized by a cluster of enhancers each of which bind a cognate transcription factor capable of interacting with Mediator to stimulate transcription of the target gene within said cell; (b) measuring in the identified genomic region a level of a super-enhancer component, e.g., Mediator; and (c) identifying the genomic region as a super enhancer, or functional fragment and/or variant thereof, if the level of Mediator is greater than the level of Mediator occupying the average single enhancer.

In some embodiments the level of a super-enhancer component, e.g., Mediator, identified in the genomic region is an order of magnitude more than the level of the super-enhancer component, e.g., Mediator, occupying the average single enhancer. In some embodiments the order of magnitude is at least 2-fold, at least 10-fold, at least 15-fold, at least 16-fold, or more.

In some embodiments the super enhancer, or functional fragment and/or variant thereof, is identified by performing chromatin immunoprecipitation high-throughput sequencing (ChIP-Seq). In some embodiments, the super-enhancer is identified by evaluation of a surrogate mark of an enhancer such as histone H3K27ac, H3K4me1, DNAse hypersensitivity or p300 (e.g., histone H3K27ac).

In an embodiment, the method further comprises identifying a gene associated with (e.g., controlled by) the super-enhancer, e.g., a gene that is regulated by the super-enhancer.

In an embodiment, the gene is identified by selecting the nearest gene to the super-enhancer as a gene associated with a super-enhancer.

In an embodiment the gene whose transcription start site (TSS) is the closest to the center point of the super-enhancer is selected as associated with the super-enhancer.

In an embodiment, the gene is identified by selecting the nearest gene that meets a preselected criteria, e.g., the nearest expressed gene. In embodiments selection criteria can be defined based on RNA data (RNA-Seq, Gro-Seq, or microarray), or ChIP-Seq of transcription-associated signals (RNA polymerase II, H3K4me3, H3K27ac levels around the transcription start site). In an embodiment, the selection criteria comprises evaluation of transcription associated signals of H3K27ac using ChIP-Seq signal around the transcription start site of the genes to define the set of expressed genes in cells. In an embodiment, an expressed gene within a certain genomic window is selected. For example, in an embodiment a maximum distance between the super-enhancer center and the transcription start site of the regulated gene is set to evaluation the gene.

In an embodiment, multiple genes are identified as being associated with (e.g., controlled by) a super-enhancer, for example, having a certain genomic window. In an embodiment, multiple genes are selected to be associated with a super-enhancer provided their transcription start site is within a certain distance to the center of the super-enhancer. In an embodiment, multiple genes are selected to be associated with a super-enhancer wherein the multiple genes expressed within a certain genomic window are selected as being associated with the super-enhancer.

In an embodiment, a gene that is the closest expressed gene within a topological domain (TD) is selected as being associated with a super-enhancer. Topological domains are architectural chromosomal units defined by chromosome conformation capture techniques (hi-C). In embodiments, genomic regions within topological domains have a significantly higher interaction frequency with other regions within the same topological domain compared to genomic regions in other topological domains and therefore, in some embodiments, enhancer-gene associations do not expand beyond topological domain boundaries. In some embodiments, multiple genes are selected as being associated with a super-enhancer within a topological domain.

In an embodiment, a gene is selected as being associated with a super-enhancer based on chromatin correlation. See, for example, Shen et al, Nature, 2012; and Maurano et al, Science, 2012. In an embodiment, an enhancer and its regulated gene display similar levels of transcription associated chromatin marks (or DNase hypersensitivity level) in cells where the enhancer is active and the gene is expressed. In an embodiment, across a range of cell types an enhancer only in one particular cell, and a gene that is expressed only in that particular cell but not in any other, can provide that that enhancer is assigned to that particular gene.

In some aspects the invention provides a method of identifying a super enhancer, or functional fragment and/or variant thereof, in a cell, comprising: (a) identifying a genomic region of DNA within said cell characterized by a cluster of enhancers each of which bind a cognate transcription factor capable of interacting with Mediator to stimulate transcription of the target gene within said cell; (b) measuring in the identified genomic region a level of RNA (e.g., eRNA); and (c) identifying the genomic region as a super enhancer, or functional fragment and/or variant thereof, if the level of RNA (e.g., eRNA) is greater than the level of RNA (e.g., eRNA) occupying the average single enhancer.

In some embodiments the level of RNA (e.g., eRNA) identified in the genomic region is an order of magnitude more than the level of RNA (e.g., eRNA) occupying the average single enhancer. In some embodiments the order of magnitude is at least 2-fold, at least 10-fold, at least 15-fold, at least 16-fold, or more.

In some embodiments the super enhancer, or functional fragment and/or variant thereof, is identified by performing high-throughput sequencing such as RNA-seq. In an embodiment, RNA-Seq data is used, after filtering out the sequencing reads that map to protein coding regions. In an embodiment, the RNA is a cellular RNA fraction containing polyA tails or total cellular RNA from which the ribosomal RNA was removed. In an embodiment, the RNA-Seq is used with a small sample, e.g., a single cell. In an embodiment, the RNA-Seq is used to identify super-enhancers in primary cells, disease cells, small tumor samples, where the number of available cells is limited.

In an embodiment, the method further comprises identifying a gene associated with (e.g., controlled by) the super-enhancer, e.g., a gene that is regulated by the super-enhancer.

In an embodiment, the gene is identified by selecting the nearest gene to the super-enhancer as a gene associated with a super-enhancer.

In an embodiment the gene whose transcription start site (TSS) is the closest to the center point of the super-enhancer is selected as associated with the super-enhancer.

In an embodiment, the gene is identified by selecting the nearest gene that meets a preselected criteria, e.g., the nearest expressed gene. In embodiments selection criteria can be defined based on RNA data (RNA-Seq, Gro-Seq, or microarray), or ChIP-Seq of transcription-associated signals (RNA polymerase II, H3K4me3, H3K27ac levels around the transcription start site). In an embodiment, the selection criteria comprises evaluation of transcription associated signals of H3K27ac using ChIP-Seq signal around the transcription start site of the genes to define the set of expressed genes in cells. In an embodiment, an expressed gene within a certain genomic window is selected. For example, in an embodiment a maximum distance between the super-enhancer center and the transcription start site of the regulated gene is set to evaluation the gene.

In an embodiment, multiple genes are identified as being associated with (e.g., controlled by) a super-enhancer, for example, having a certain genomic window. In an embodiment, multiple genes are selected to be associated with a super-enhancer provided their transcription start site is within a certain distance to the center of the super-enhancer. In an embodiment, multiple genes are selected to be associated with a super-enhancer wherein the multiple genes expressed within a certain genomic window are selected as being associated with the super-enhancer.

In an embodiment, a gene that is the closest expressed gene within a topological domain (TD) is selected as being associated with a super-enhancer. Topological domains are architectural chromosomal units defined by chromosome conformation capture techniques (hi-C). In embodiments, genomic regions within topological domains have a significantly higher interaction frequency with other regions within the same topological domain compared to genomic regions in other topological domains and therefore, in some embodiments, enhancer-gene associations do not expand beyond topological domain boundaries. In some embodiments, multiple genes are selected as being associated with a super-enhancer within a topological domain.

In an embodiment, a gene is selected as being associated with a super-enhancer based on chromatin correlation. See, for example, Shen et al, Nature, 2012; and Maurano et al, Science, 2012. In an embodiment, an enhancer and its regulated gene display similar levels of transcription associated chromatin marks (or DNase hypersensitivity level) in cells where the enhancer is active and the gene is expressed. In an embodiment, across a range of cell types an enhancer only in one particular cell, and a gene that is expressed only in that particular cell but not in any other, can provide that that enhancer is assigned to that particular gene.

In some aspects the invention provides a method of identifying a super enhancer, or functional fragment and/or variant thereof, in a cell, comprising: (a) identifying a genomic region of DNA within said cell characterized by a cluster of enhancers each of which bind a cognate transcription factor capable of interacting with Mediator to stimulate transcription of the target gene within said cell; (b) measuring in the identified genomic region a level of nucleic acid (e.g., RNA, eRNA); and (c) identifying the genomic region as a super enhancer, or functional fragment and/or variant thereof, if the level of nucleic acid (e.g., RNA, eRNA) is greater than the level of nucleic acid (e.g., RNA, eRNA) occupying the average single enhancer.

In some embodiments the level of nucleic acid (e.g., RNA, eRNA) identified in the genomic region is an order of magnitude more than the level of nucleic acid (e.g., RNA, eRNA) occupying the average single enhancer. In some embodiments the order of magnitude is at least 2-fold, at least 10-fold, at least 15-fold, at least 16-fold, or more.

In some embodiments the super enhancer, or functional fragment and/or variant thereof, is identified by performing high-throughput sequencing such as GRO-Seq (See, e.g., Core, Waterfall and Lis, Science, 2009. In an embodiment, GRO-Seq measures the distribution of transcriptional activity across the genome and works the following way: A ribonucleotide analog (5′bromouridine 5′triphophate (BrUTP)) is added to the cells for a short period of time, and this analog gets incorporated into RNA (instead of uridine). This labeled pool of RNA is purified with an antibody specific against BrUTP, sequenced, and mapped to the genome.

In an aspect, the invention features a method of modulating the structure or activity of a super-enhancer. The method comprises:

a) altering the level or proportion of a super-enhancer component;

b) altering the activity of a super-enhancer component;

c) altering the ability of a super-enhancer component to bind to or interact with another super-enhancer component, e.g., another super-enhancer component or DNA or chromatin, or a component of basal transcriptional machinery;

d) altering the interaction between a super-enhancer component and a component at a site outside the superenhancer, e.g., a site of transcription initiation; or

e) altering the ability of the super-enhancer to loop to another component, e.g., outside the super-enhancer; thereby modulating the structure or activity of a super-enhancer.

In some embodiments, the method comprises reducing or inhibiting the activity of the super-enhancer, e.g. using a method described herein. In some embodiments, the method comprises disrupting the structure of a superenhancer.

In some aspects, the invention provides a method of selectively inhibiting expression of an aberrantly expressed gene comprising disrupting the function of a super-enhancer associated with the aberrantly expressed gene.

In some embodiments the gene is an oncogene. In some embodiments the oncogene is selected from the group consisting of c-MYC and IRF4.

In some embodiments, the gene is associated with a hallmark of a disease such as cancer. In some embodiments, the gene has a disease associated DNA sequence variation such as a SNP. In some embodiments, the disease is Alzheimer's disease, and the gene is BIN1 (e.g., having a disease associated DNA sequence variation such as a SNP). In some embodiments, the disease is type 1 diabetes, and the gene is associated with a primary Th cell (e.g., having a disease associated DNA sequence variation such as a SNP). In some embodiments, the disease is systemic lupus erythematosus, and the gene plays a key role in B cell biology (e.g., having a disease associated DNA sequence variation such as a SNP). In some embodiments, the gene is associated with a hallmark characteristic of the cell. In some embodiments, the gene is aberrantly expressed or is associated with a DNA variation such as a SNP. In some embodiments, the cell or tissue includes one of the following: mammalian cell, e.g., human cell; fetal cell; embryonic stem cell or embryonic stem cell-like cell, e.g., cell from the umbilical vein, e.g., endothelial cell from the umbilical vein; muscle, e.g., myotube, fetal muscle; blood cell, e.g., cancerous blood cell, fetal blood cell, monocyte; B cell, e.g., Pro-B cell; brain, e.g., astrocyte cell, angular gyms of the brain, anterior caudate of the brain, cingulate gyms of the brain, hippocampus of the brain, inferior temporal lobe of the brain, middle frontal lobe of the brain, brain cancer cell; T cell, e.g., naïve T cell, memory T cell; CD4 positive cell; CD25 positive cell; CD45RA positive cell; CD45RO positive cell; IL-17 positive cell; a cell that is stimulated with PMA; Th cell; Th17 cell; CD255 positive cell; CD127 positive cell; CD8 positive cell; CD34 positive cell; duodenum, e.g., smooth muscle tissue of the duodenum; skeletal muscle tissue; myoblast; stomach, e.g., smooth muscle tissue of the stomach, e.g., gastric cell; CD3 positive cell; CD14 positive cell; CD19 positive cell; CD20 positive cell; CD34 positive cell; CD56 positive cell; prostate, e.g., prostate cancer; colon, e.g., colorectal cancer cell; crypt cell, e.g., colon crypt cell; intestine, e.g., large intestine; e.g., fetal intestine; bone, e.g., osteoblast; pancreas, e.g., pancreatic cancer; adipose tissue; adrenal gland; bladder; esophagus; heart, e.g., left ventricle, right ventricle, left atrium, right atrium, aorta; lung, e.g., lung cancer cell; skin, e.g., fibroblast cell; ovary; psoas muscle; sigmoid colon; small intestine; spleen; thymus, e.g., fetal thymus; breast, e.g., breast cancer; cervix, e.g., cervical cancer; mammary epithelium; liver, e.g., liver cancer; DND41 cell; GM12878 cell; H1 cell; H2171 cell; HCC1954 cell; HCT-116 cell; HeLa cell; HepG2 cell; HMEC cell; HSMM tube cell; HUVEC cell; IMR90 cell; Jurkat cell; K562 cell; LNCaP cell; MCF-7 cell; MM1S cell; NHLF cell; NHDF-Ad cell; RPMI-8402 cell; U87 cell; VACO 9M cell; VACO 400 cell; or VACO 503 cell.

In some embodiments, the gene comprises a disease-associated variation related to rheumatoid arthritis, multiple sclerosis, systemic scleroderma, primary biliary cirrhosis, Crohn's disease, Graves disease, vitiligo and atrial fibrillation.

In some embodiments disrupting the function of the super-enhancer comprises contacting said super-enhancer region with an effective amount of an agent that interferes with occupancy of the super-enhancer region by a cognate transcription factor for the gene, a transcriptional coactivator, or a chromatin regulator. In some embodiments the agent is a bromodomain inhibitor. In some embodiments the agent is a BRD4 inhibitor.

In some embodiments the agent is JQ1.

In some embodiments the agent is iBET. In some embodiments the agent interferes with a binding site on the super-enhancer for the cognate transcription factor, interferes with interaction between the cognate transcription factor and a transcriptional coactivator, inhibits the transcription coactivator, or interferes with or inhibits the chromatin regulator.

In some aspects the invention provides a method of treating a proliferative disorder in a patient in need of such treatment, said proliferative disorder characterized by an oncogene-associated super-enhancer occupied by more Mediator or BRD4 than an average single enhancer, comprising administering to the patient an effective amount of an agent that disrupts the function of the oncogene-associated super-enhancer, thereby selectively inhibiting proliferation of the oncogene in the patient.

In some embodiments the proliferative disorder is a hematological malignancy.

In some embodiments the proliferative disorder is selected from the group consisting of acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), chronic lymphocytic leukemia (CLL), hairy cell leukemia, Hodgkin's lymphoma, non-Hodgkin's lymphoma, cutaneous T-cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), Mantle cell lymphoma, B-cell lymphoma, acute lymphoblastic T cell leukemia (T-ALL), acute promyelocytic leukemia, and multiple myeloma.

In some embodiments the agent is a BRD4 inhibitor. In some embodiments the agent is JQ1. In some embodiments the agent is iBET.

In some aspects, the invention provides a method of treating multiple myeloma involving an IGH-MYC locus that results in aberrant expression of oncogene c-Myc, comprising administering to a patient in need of such treatment an effective amount of an agent that decreases occupancy levels of BRD4 and MED1 at a super-enhancer region associated with the IGH-MYC locus, wherein decreased occupancy levels of BRD4 and MED1 at the super-enhancer disrupt function of the super-enhancer thereby decreasing aberrant expression of oncogene c-Myc such that the multiple myeloma is treated. In some embodiments the agent is JQ1 or iBET.

In some embodiments, the invention provides a method of treating Alzheimer's disease. In some embodiments, the Alzheimer's disease is associated with DNA sequence variation such as a SNP, for example in a gene such as BIN1.

In some embodiments, the invention provides a method of treating type 1 diabetes. In some embodiments, the type 1 diabetes is associated with DNA sequence variation such as a SNP, for example in a gene associated with a primary Th cell.

In some embodiments, the invention provides a method of treating systemic lupus erythematosus. In some embodiments, the systemic lupus erythematosus is associated with DNA sequence variation such as a SNP, for example in a gene having a key role in B cell biology.

In some embodiments, the gene comprises a disease-associated variation related to rheumatoid arthritis, multiple sclerosis, systemic scleroderma, primary biliary cirrhosis, Crohn's disease, Graves disease, vitiligo and atrial fibrillation. In some embodiments, a disease-associated variation is present in one or more of the following cells or tissues: mammalian cell, e.g., human cell; fetal cell; embryonic stem cell or embryonic stem cell-like cell, e.g., cell from the umbilical vein, e.g., endothelial cell from the umbilical vein; muscle, e.g., myotube, fetal muscle; blood cell, e.g., cancerous blood cell, fetal blood cell, monocyte; B cell, e.g., Pro-B cell; brain, e.g., astrocyte cell, angular gyms of the brain, anterior caudate of the brain, cingulate gyms of the brain, hippocampus of the brain, inferior temporal lobe of the brain, middle frontal lobe of the brain, brain cancer cell; T cell, e.g., naïve T cell, memory T cell; CD4 positive cell; CD25 positive cell; CD45RA positive cell; CD45RO positive cell; IL-17 positive cell; a cell that is stimulated with PMA; Th cell; Th17 cell; CD255 positive cell; CD127 positive cell; CD8 positive cell; CD34 positive cell; duodenum, e.g., smooth muscle tissue of the duodenum; skeletal muscle tissue; myoblast; stomach, e.g., smooth muscle tissue of the stomach, e.g., gastric cell; CD3 positive cell; CD14 positive cell; CD19 positive cell; CD20 positive cell; CD34 positive cell; CD56 positive cell; prostate, e.g., prostate cancer; colon, e.g., colorectal cancer cell; crypt cell, e.g., colon crypt cell; intestine, e.g., large intestine; e.g., fetal intestine; bone, e.g., osteoblast; pancreas, e.g., pancreatic cancer; adipose tissue; adrenal gland; bladder; esophagus; heart, e.g., left ventricle, right ventricle, left atrium, right atrium, aorta; lung, e.g., lung cancer cell; skin, e.g., fibroblast cell; ovary; psoas muscle; sigmoid colon; small intestine; spleen; thymus, e.g., fetal thymus; breast, e.g., breast cancer; cervix, e.g., cervical cancer; mammary epithelium; liver, e.g., liver cancer; DND41 cell; GM12878 cell; H1 cell; H2171 cell; HCC1954 cell; HCT-116 cell; HeLa cell; HepG2 cell; HMEC cell; HSMM tube cell; HUVEC cell; IMR90 cell; Jurkat cell; K562 cell; LNCaP cell; MCF-7 cell; MM1S cell; NHLF cell; NHDF-Ad cell; RPMI-8402 cell; U87 cell; VACO 9M cell; VACO 400 cell; or VACO 503 cell.

In some aspects the invention provides a method of identifying an agent that modulates (e.g., disrupts) a super-enhancer associated with a gene, e.g., a super-enhancer identified by a method described herein, comprising:

(a) providing a cell or cell-free system having a super-enhancer, or functional fragment and/or variant thereof, associated with a gene, e.g., a gene which is heterologous to one or both of the cell or the super-enhancer, e.g., a reporter construct;

(b) contacting the cell with a test agent, e.g., under conditions suitable for the super-enhancer, or functional fragment and/or variant thereof, to drive high levels of expression of the associated gene; and

(c) measuring the level of expression of the associated gene, e.g., a reporter construct.

In an embodiment decreased expression of the associated gene in the presence of the test agent indicates that the test agent is as an agent that disrupts the super-enhancer associated with the gene.

In an embodiment the method comprises comparing the level of expression with a reference, e.g., a similar cell or cell-free system not contacted with the test agent.

In an embodiment the method comprises confirming disruption of the super-enhancer, or functional fragment and/or variant thereof, e.g., by analysis of the presence of one or more super-enhancer component.

In an embodiment the method is first performed in a cell-free system or a cell preparation, e.g., a cultured cell, and repeated in an animal.

In an embodiment the super-enhancer is associated with a gene that is expressed in a disease state cell, e.g., a cancer cell.

The method, as well as any other method described herein, can include memorializing the results.

In some aspects the invention provides a method of identifying an agent that modulates (e.g., disrupts) a super-enhancer associated with a gene, comprising:

(a) providing a cell or cell-free system having a heterologous super-enhancer, or functional fragment and/or variant thereof, associated with a gene, e.g., a gene which is heterologous to one or both of the cell or the super-enhancer, e.g., a reporter construct;

(b) contacting the cell or cell-free system with a test agent, e.g., under conditions suitable for the super-enhancer, or functional fragment and/or variant thereof, to drive high levels of expression of the associated gene;

(c) and measuring the level of expression of the associated gene, e.g., a reporter construct.

In an embodiment decreased expression of the associated gene in the presence of the test agent indicates that the test agent is as an agent that disrupts the super-enhancer associated with the gene.

In an embodiment the method comprises comparing the level of expression with a reference, e.g., a similar cell or cell-free system not contacted with the test agent.

In an embodiment the method comprises confirming disruption of the super-enhancer, or functional fragment and/or variant thereof, e.g., by analysis of the presence of one or more super-enhancer component.

In an embodiment the method is first performed in a cell-free system or a cell preparation, e.g., a cultured cell, and repeated in an animal.

In an embodiment the super-enhancer is associated with a gene that is expressed in a disease state cell, e.g., a cancer cell. In an embodiment, the gene is an oncogene (e.g., c-Myc). In an embodiment, the gene has a DNA sequence variation such as a SNP.

In some aspects the invention provides a method of identifying an agent that modulates (e.g., disrupts) a super-enhancer associated with a gene, comprising: (a) transfecting a cell with a super-enhancer, or functional fragment and/or variant thereof, and the associated gene under conditions suitable for the super-enhancer to drive high levels of expression of the associated gene; (b) contacting the cell with a test agent; (c) and measuring the level of expression of the associated gene, wherein decreased expression of the associated gene in the presence of the test agent indicates that the test agent is as an agent that disrupts the super-enhancer associated with the gene.

In an embodiment the method comprises comparing the level of expression with a reference, e.g., a similar cell not contacted with the test agent. In an embodiment the method comprises confirming disruption of the super-enhancer, or functional fragment and/or variant thereof, e.g., by analysis of the presence of one or more super-enhancer component. In an embodiment the method is first performed in a cell-free system or a cell preparation, e.g., a cultured cell, and repeated in an animal.

In an embodiment the super-enhancer is associated with a gene that is expressed in a disease state cell, e.g., a cancer cell.

In some aspects the invention provides a method of identifying an agent that modulates (e.g., disrupts) a super-enhancer comprising: (a) transfecting a cell with a super-enhancer operably linked to a reporter construct comprising a reporter gene under conditions suitable for the super-enhancer to drive high levels of expression of the reporter gene; (b) contacting the cell with a test agent; (c) and measuring the level of expression of the reporter gene, wherein decreased expression of the reporter gene in the presence of the test agent indicates that the test agent is as an agent that disrupts the super-enhancer.

In some embodiments the super-enhancer is naturally associated with a gene of interest, wherein the gene of interest is optionally a disease-associated gene, optionally an oncogene. In some embodiments expression is measured at least in part by measuring the level of a gene product encoded by the gene or by measuring activity of a gene product encoded by the gene. In some embodiments a gene product is mRNA or polypeptide encoded by the gene.

In some aspects, the invention relates to a method of identifying a super-enhancer, or a gene associated with a super-enhancer, comprising:

cross-linking, e.g., covalently cross-linking, chromatin, such that chromosomal nucleic acid is cross-linked to a super-enhancer component, e.g., a chromatin associated protein, e.g., one or more of a Mediator protein, Med1, Oct4, Sox2, Nanog, or NOS, to form a cross-linked complex, e.g., an RNA such as an eRNA;

contacting said cross-linked complex with a ligand having affinity for the super-enhancer component, e.g., an antibody or small molecule with affinity for the super-enhancer component to form a complex between the cross-linked complex and the ligand;

optionally, identifying or sequencing chromosomal nucleic acid in the complex between the cross-linked complex and the ligand, thereby identifying a super-enhancer, or a gene associated with a super-enhancer.

In some embodiments, the super-enhancer component comprises RNA polymerase II, Mediator, cohesin, Nipb1, p300, CBP, Chd7, Brd4, and components of the esBAF (Brg1) or a Lsd1-Nurd complex (e.g., RNA polymerase II).

In some embodiments, the super-enhancer component comprises one or more of Nr5a2, Prdm14, Tcfcp211, Smad3, Stat3 or Tcf3. In some embodiments, the super-enhancer component comprises Oct 4, Sox2, Nanog, Klf4, Esrrb, Nr5a2, Prdm14, Tcfcp211, Smad3, Stat3 or Tcf3. In some embodiments, the transcription factor is directly down to its known DNA sequence motif.

In an embodiment the method comprises fragmenting the chromosomal nucleic acid, e.g., after the step of forming a cross-linked complex, or after forming the complex between the cross-linked complex and the ligand.

In embodiments the method comprises identifying a gene associated with the super-enhancer.

In embodiments the method comprises classifying an enhancer as having a first or second level of occupancy, wherein said first level is higher, e.g., 2, 5, 10, or 100 times higher than the second level.

In some aspects, the invention relates to a method of identifying a super-enhancer, or a gene associated with a super-enhancer, comprising:

identifying sites on a segment of chromosome that are hypersensitive to reaction with an agent, e.g., a nuclease, e.g., a DNase, e.g., DNase I;

identifying or sequencing chromosomal nucleic acid adjacent the sites; thereby identifying a super-enhancer, or a gene associated with a super-enhancer.

In an embodiment the method comprises fragmenting the chromosomal nucleic acid, e.g., after the step of forming a cross-linked complex, or after forming the complex between the cross-linked complex and the ligand.

In embodiments the method comprises identifying a gene associated with the super-enhancer.

In an embodiment, the method comprises confirmint, e.g., by sequencing, that a candidate super-enhancer site comprises a plurality of enhancers.

In embodiments the method comprises classifying an enhancer as having a first or second level of occupancy, wherein said first level is higher, e.g., 2, 5, 10, or 100 times higher than the second level.

In another aspect, the invention features a method of selecting a gene, e.g., to target for upregulation or inhibition. The method comprises acquiring knowledge of whether the gene is regulated by a superenhancer, wherein if the gene is regulated by a superenhancer, then selecting the gene. In an embodiment, the gene is a gene described herein. In an embodiment, the superenhancer comprises a preselected genetic signature. In an embodiment, the gene is a gene selected from one of Tables 1-90.

In another aspect, the invention features, a method of evaluating a subject, e.g., a patient. The method comprises acquiring, e.g., directly or indirectly, knowledge whether a superenhancer is present at a preselected gene (e.g., a gene described herein such as a gene described in any of Tables 1-90); and optionally, responsive to said determination, selecting a course of therapy for said patient.

In some embodiments, wherein a super-enhancer is determined to be present at a specified gene, the course of action comprises administering to a subject a compound that modulates, e.g., disrupts the structure or activity of the super-enhancer.

In another aspect, the invention features a method of determining if a genetic signature (a genetic signature, as used herein can comprise an SNP, mutation, rearrangement, e.g., an insertion, translocation, or deletion) occurs in a super-enhancer. The method comprises:

a) acquiring, e.g., directly or indirectly, knowledge of whether, said genetic signature is present in a super-enhancer sequence, e.g., a chromosomal sequence at which a super-enhancer has been found; and

optionally, b) acquiring knowledge of whether super-enhancer is present at said nucleic acid sequence.

As used herein, “acquire” or “acquiring” refers to obtaining possession of a physical entity, or a value, e.g., a numerical value, by “directly acquiring” or “indirectly acquiring” the physical entity or the value. “Directly acquiring” means performing a process (e.g., performing an assay or test on a sample or “analyzing a sample” as that term is defined herein) to obtain the physical entity or value. “Indirectly acquiring” refers to receiving the physical entity or value from another party or source (e.g., a third party laboratory that directly acquired the physical entity or value). Directly acquiring a physical entity includes performing a process, e.g., analyzing a sample, that includes a physical change in a physical substance, e.g., a starting material. Exemplary changes include making a physical entity from two or more starting materials, shearing or fragmenting a substance, separating or purifying a substance, combining two or more separate entities into a mixture, performing a chemical reaction that includes breaking or forming a covalent or non-covalent bond. Directly acquiring a value includes performing a process that includes a physical change in a sample or another substance, e.g., performing an analytical process which includes a physical change in a substance, e.g., a sample, analyte, or reagent (sometimes referred to herein as “physical analysis”), performing an analytical method, e.g., a method which includes one or more of the following: separating or purifying a substance, e.g., an analyte, or a fragment or other derivative thereof, from another substance; combining an analyte, or fragment or other derivative thereof, with another substance, e.g., a buffer, solvent, or reactant; or changing the structure of an analyte, or a fragment or other derivative thereof, e.g., by breaking or forming a covalent or non-covalent bond, between a first and a second atom of the analyte; or by changing the structure of a reagent, or a fragment or other derivative thereof, e.g., by breaking or forming a covalent or non-covalent bond, between a first and a second atom of the reagent.

In an embodiment at least one of a or b is directly acquired.

In an embodiment the super-enhancer is a superenhancer described herein, for example, in any of tables 1-90, e.g., in a cell type or tissue described herein.

In an embodiment the method comprises one or more of memorializing the result of said determination and communicating the result to another entity.

In another aspect, the invention features a method of evaluating a genetic signature, e.g., a mutation or SNP. The method comprises:

a) acquiring, e.g., directly or indirectly, knowledge of whether, said genetic signature is present in a super-enhancer sequence, e.g., a chromosomal at which a super-enhancer has been found; and

optionally, b) acquiring knowledge of whether super-enhancer is present at said nucleic acid sequence.

In an embodiment at least one of a or b is directly acquired.

In an embodiment the super-enhancer is a super-enhancer described herein, for example, in any of tables 1-90, e.g., in a cell type or tissue described herein.

In an embodiment the method comprises one or more of memorializing the result of said evaluation and communicating the result to another entity.

In an embodiment the method comprises acquiring knowledge of whether the genetic signature is present on a plurality of subjects.

In an embodiment the method comprises acquiring knowledge of whether the genetic signature in a subject having a disorder and a subject not having the disorder, and optionally, correlating the genetic signature with the disorder.

A method of evaluating a nucleic acid sample, e.g. a sample comprising genomic DNA from a subject comprising:

optionally, providing a sample;

a) acquiring, e.g., directly or indirectly, the sequence of all or part of at least 1, 2, 3, 4, 5, 10, 15, 25, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 500, or 1000 superenhancer; and

optionally, b) acquiring, e.g., directly or indirectly, a determination of whether a preselected genetic signature, e.g., an SNP or mutation, is present on one of said super-enhancer s,

thereby evaluating said nucleic acid sample.

In an embodiment at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 95% of the sequence of an super-enhancer is determined.

In an embodiment a preselected region of a SE, but not the entire super-enhancer, is sequenced.

In an embodiment at least one of a or b is directly acquired.

In an embodiment the superenhancer is a super-enhancer described herein, for example, in any of tables 1-90, e.g., in a cell type or tissue described herein.

In an embodiment the method comprises one or more of memorializing the result of said evaluation and communicating the result to another entity.

A method of evaluating a subject, comprising:

optionally, providing a sample comprising genomic DNA, e.g., from a disease state tissue;

a) acquiring, e.g., directly or indirectly, the sequence of all or part of at least 1, 2, 3, 4, 5, 10, 15, 25, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 500, or 1000 super-enhancers in said DNA; and

optionally, b) acquiring, e.g., directly or indirectly, a determination of whether a preselected genetic signature, e.g., an SNP or mutation, is present on one of said superenhancers;

thereby evaluating said nucleic acid sample.

In an embodiment at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 95% of the sequence of a super-enhancer is determined.

In an embodiment a preselected region of a super-enhancer, but not the entire super-enhancer, is sequenced.

In an embodiment at least one of a or b is directly acquired.

In an embodiment the super-enhancer is a super-enhancer described herein, for example, in any of tables 1-90, e.g., in a cell type or tissue described herein.

In an embodiment the method comprises one or more of memorializing the result of said evaluation and communicating the result to another entity.

The practice of the present invention will typically employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant nucleic acid (e.g., DNA) technology, immunology, and RNA interference (RNAi) which are within the skill of the art. Non-limiting descriptions of certain of these techniques are found in the following publications: Ausubel, F., et al., (eds.), Current Protocols in Molecular Biology, Current Protocols in Immunology, Current Protocols in Protein Science, and Current Protocols in Cell Biology, all John Wiley & Sons, N.Y., edition as of December 2008; Sambrook, Russell, and Sambrook, Molecular Cloning: A Laboratory Manual, 3^(rd) ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 2001; Harlow, E. and Lane, D., Antibodies—A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1988; Freshney, R. I., “Culture of Animal Cells, A Manual of Basic Technique”, 5th ed., John Wiley & Sons, Hoboken, N.J., 2005. Non-limiting information regarding therapeutic agents and human diseases is found in Goodman and Gilman's The Pharmacological Basis of Therapeutics, 11th Ed., McGraw Hill, 2005, Katzung, B. (ed.) Basic and Clinical Pharmacology, McGraw-Hill/Appleton & Lange; 10^(th) ed. (2006) or 11th edition (July 2009). Non-limiting information regarding genes and genetic disorders is found in McKusick, V. A.: Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders. Baltimore: Johns Hopkins University Press, 1998 (12th edition) or the more recent online database: Online Mendelian Inheritance in Man, OMIM™. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, Md.) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, Md.), as of May 1, 2010, World Wide Web URL: http://www.ncbi.nlm.nih.gov/omim/ and in Online Mendelian Inheritance in Animals (OMIA), a database of genes, inherited disorders and traits in animal species (other than human and mouse), at http://omia.angis.org.au/contact.shtml. All patents, patent applications, and other publications (e.g., scientific articles, books, websites, and databases) mentioned herein are incorporated by reference in their entirety. In case of a conflict between the specification and any of the incorporated references, the specification (including any amendments thereof, which may be based on an incorporated reference), shall control. Standard art-accepted meanings of terms are used herein unless indicated otherwise. Standard abbreviations for various terms are used herein.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and payment of the necessary fee.

FIGS. 1(A)-1(D) show that Oct4/Sox2/Nanog define enhancers in ES cells. (FIG. 1A) Example enhancer upstream of the Hkt2 gene. (FIG. 1B) Example of super-enhancer upstream of the Klf4 gene. (FIG. 1C) Scatter plot of Mediator occupancy across the ˜6,400 ESC enhancers. (FIG. 1D) Metagenes of Med1 at typical and super-enhancers in ESCs.

FIGS. 2(A)-2(D) illustrate that super-enhancers drive key pluripotency genes. (FIG. 2A) Super-enhancers drive highly expressed genes. (FIG. 2B) Example of typical enhancer-associated gene (with RNA-seq). (FIG. 2C) Example of super-enhancer-associated gene (with RNA-seq) (FIG. 2D) Super-enhancers associate with the ESC master regulators Oct4, Sox2 and Nanog.

FIGS. 3(A)-3(C) illustrate that super-enhancers confer high enhancer activity. (FIG. 3A) OSN and Mediator gene tracks at enhancers near Klf4 (super-enhancer associated gene), and Egln3 (typical enhancer-associated gene), and corresponding DNA binding motifs. (FIG. 3B) Super-enhancers have high enhancer activity in vitro. 3000 bp genomic fragments were cloned into a luciferase reporter plasmid. Luciferase activity was measured 24 hours post transfection, and was normalized to a co-transfected control plasmid. (FIG. 3C) Creation of artificial super-enhancers by clustering. Single enhancers were genetically oligomerized and cloned into luciferase reporters. Luciferase activity was measured 24 hours post transfection, and was normalized to a co-transfected control plasmid.

FIGS. 4(A)-4(B) show rapid loss of ESC super-enhancers and establishment of new super-enhancers during ESC differentiation. (FIG. 4A) Cartoon diagram depicting treatment of ZHBTc4 ESCs with doxycycline leading to loss of Oct4 proteins, loss of ESC state, and formation of early trophectoderm cells. (FIG. 4B) Mediator is rapidly lost at key ESC super-enhancers compared to median enhancers. Bar graphs of mean normalized Med1 density before and during ESC differentiation at selected ESC super-enhancers and median enhancers. The associated genes were identified based on their proximity to the enhancers. Asterisks denote enhancers displaying at least two-fold reduction in Mediator.

FIGS. 5(A)-5(E) illustrate that super-enhancers are a general feature of mammalian cells and are cell-type specific. (FIG. 5A) Pro-B enhancers are associated with the gene Rag1. ChIP-Seq binding profiles (normalized reads/million) for the pro-B transcription factor (Pu.1), and the Mediator coactivator (Med1) at the Rag1 locus in pro-B cells, with the y-axis floor set to 1. Gene model, and previously described enhancer regions are depicted below the binding profiles. (FIG. 5B) Pro-B super-enhancers are associated with the key pro-B gene Inpp5d. ChIP-Seq binding profiles (normalized reads/million) for the pro-B transcription factor (Pu.1), and the Mediator coactivator (Med1) at the Inpp5d locus in pro-B cells, with the y-axis floor set to 1. Gene model, and previously described enhancer regions are depicted below the binding profiles. (FIG. 5C) Scatter plot of Mediator occupancy across the ˜13000 pro-B enhancers. (FIG. 5D) Master transcription factors (Oct4 for ESCs; Pu.1 for pro-B cells) and Mediator occupy approximately super-enhancer regions that are specific for ESCs and pro-B cells. Density maps of the Mediator coactivator (Med1) in ESCs and pro-B cells. Color scale reflects ChIP-Seq signal in reads per million. (FIG. 5E) Super-enhancer associated genes display highly cell-type specific patterns of expression. Venn diagram of ESC super-enhancer-associated genes and pro-B super-enhancer-associated genes.

FIGS. 6(A)-6(D) show that Mediator and BRD4 co-occupy promoters of active genes in multiple myeloma. (FIG. 6A) Gene tracks of BRD4, MED1, H3K27ac, and H3K4me3 binding at the XBP1 gene in MM.1S multiple myeloma. (FIG. 6B) Metagene representation of global BRD4, MED1, H3K27ac, and H3K4me3 occupancy at enhancers and promoters. The top 5,000 active enhancers are defined by MED1 occupancy, and TSS includes all transcriptionally active promoters defined by H3K4me3 and POL2. (FIG. 6C) Mediator and BRD4 occupancy correlate with one another at both enhancers and transcription start sites. Scatter plots depicting MED1 and BRD4 aggregate signal+/−5 kb from enhancers and promoters (as defined in 1B). (FIG. 6D) BRD4 occupancy at genes correlates with RNAPII levels.

FIGS. 7(A)-7(D) show that super-enhancers are associated with key multiple myeloma genes. (FIG. 7A) The sizes of enhancers occupied by Mediator show an unusual distribution. (FIG. 7B) Occupancy of MED1, BRD4, and H3K27ac at super-enhancers compared to normal enhancers. (FIG. 7C) Super-enhancers are associated with highly expressed, cell type specific genes. (FIG. 7D) The IgH-MYC locus and IRF4 contain a large super-enhancers occupied by high levels of BRD4 and MED1.

FIGS. 8(A)-8(F) show that BRD4 occupancy at super-enhancers is highly sensitive to bromodomain inhibition. (FIG. 8A) Measuring the effects of various concentrations of JQ1 on genome-wide on BRD4 occupancy. Schematic depicting the experimental procedure. (FIG. 8B) Short-term JQ1 treatment (6 hours) has little effect on MM.1S cell viability. JQ1 sensitivity of MM.1S cells by measurement of ATP levels (CellTiterGlo) after 6 hours of treatment. (FIG. 8C) c-Myc protein levels are significantly depleted by JQ1 treatment. Western blot of relative c-MYC levels after 6 hours of JQ1 or DMSO treatment. (FIG. 8D) JQ1 does not alter BRD4 levels or ChIP-efficency. Western blot of relative BRD4 levels after 6 hours of JQ1 or DMSO treatment. ChIP-Western blot of the relative levels of immunoprecipitated BRD4 after 6 hours of JQ1 or DMSO treatment. (FIG. 8E) Super-enhancers show a greater loss of BRD4 occupancy when compared to regions with average or low amounts of BRD4. (FIG. 8F) The IgH enhancer shows significantly greater loss of BRD4 than regions with lower BRD4 occupancy. Gene tracks of BRD4 at the IGH super enhancer and the average, CD28 enhancer after 6 hours of DMSO or JQ1 treatment.

FIGS. 9(A)-9(C) illustrate that loss of P-TEFb accompanies BRD4 inhibition. (FIG. 9A) P-TEFb generally occupies enhancers bound by Mediator and BRD4 in MM1.S cells. (FIG. 9B) Loss of BRD4 following JQ1 treatment is accompanied by loss of P-TEFb at enhancers. (FIG. 9C) P-TEFb is disproportionally lost at super-enhancers.

FIGS. 10(A)-10(C) show that JQ1 causes disproportionate loss of transcription at super-enhancer genes. (FIG. 10A) JQ1 leads to a global defect in transcription elongation. (FIG. 10B) Genes associated with super-enhancers show a dramatic defect in elongation. Gene tracks of RNA PolII occupancy at the MYC gene after 6 hour treatment with JQ1. (FIG. 10C) Genes associated with super enhancers show a larger increase in travelling ratio in response to JQ1 compared to genes associated with normal enhancers.

FIGS. 11(A)-11(G) show transcription factors at super-enhancers. (FIG. 11A) Distribution of Med1 ChIP-Seq signal at enhancers reveals two classes of enhancers in ESCs. (FIG. 11B) ChIP-Seq binding profiles for the indicated transcription factors at the POLE4 and miR-290-295 loci in ESCs. (FIG. 11C) Metagene representations of the mean ChIP-Seq signal for the indicated transcription factors across typical enhancers and super-enhancer domains. (FIG. 11D) Fold difference values of ChIP-Seq signal between typical enhancers and super-enhancers for the indicated transcription factors. (FIG. 11E) Metagene representations of the mean ChIP-Seq density for the indicated transcription factors across the constituent enhancers within typical enhancers and super-enhancers. (FIG. 11F) Table depicting transcription factor binding motifs enriched at constituent enhancers within super-enhancer regions, and associated p-values. (FIG. 11G) Revised model of the core transcriptional regulatory circuitry of ESCs.

FIGS. 12(A)-12(E) show RNA Polymerase II, co-factors and chromatin regulators at super-enhancers. (FIG. 12A) ChIP-Seq binding profiles for RNA Polymerase II (RNAPII) and the indicated transcriptional co-factors and chromatin regulators at the POLE4 and miR-290-295 loci in ESCs. (FIG. 12B) Metagene representations of the mean ChIP-Seq signal for RNAPII and the indicated transcriptional co-factors and chromatin regulators across typical enhancers and super-enhancer domains. (FIG. 12C) Fold difference values of ChIP-Seq signal between typical enhancers and super-enhancers for RNAPII and the indicated transcriptional co-factors and chromatin regulators, and RNA-Seq. (FIG. 12D) Metagene representations of the mean ChIP-Seq density for RNAPII and the indicated transcriptional co-factors and chromatin regulators across the constituent enhancers within typical enhancers and super-enhancers. (FIG. 12E) Model showing RNAPII, transcriptional co-factors and chromatin regulators that are found in ESC super-enhancers.

FIGS. 13(A)-13(C) show super-enhancers and candidate master transcription factors in many cell types. (FIG. 13A) Heatmap showing the classification of super-enhancer domains across 26 human cell and tissue types. (FIG. 13B) Gene Ontology terms for super-enhancer-associated genes in 14 human cell and tissue types with corresponding p-values. (FIG. 13C) Candidate master transcription factors identified in 6 cell types.

FIGS. 14(A)-14(B) show disease-associated DNA sequence variation in super-enhancers. (FIG. 14A) Catalogue of single nucleotide polymorphisms (SNP) linked to phenotypic traits and diseases in genome wide association studies (GWAS). (FIG. 14B) Radar plots showing the density of trait-associated non-coding SNPs linked to the highlighted traits and diseases, in the super-enhancer domains identified in 12 human cell and tissue types.

FIGS. 15(A)-15(C) provide examples of disease-associated SNPs in super-enhancers. (FIG. 15A) (top left) Radar plots showing the density of non-coding SNPs linked to Alzheimer's disease (AD) in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types. (top right) Distribution of non-coding SNPs linked to AD in the typical enhancers and super-enhancers of brain tissue. (bottom left) List of genes associated with AD SNP-containing super-enhancers in brain tissue. (bottom right) ChIP-Seq binding profile for H3K27ac at the BIN1 locus in brain tissue. (FIG. 15B) (top left) Radar plots showing the density of non-coding SNPs linked to type 1 diabetes (T1D) in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types. (top right) Distribution of non-coding SNPs linked to T1D in the typical enhancers and super-enhancers of Th cells. (bottom left) List of genes associated with T1D SNP-containing super-enhancers in Th cells. (bottom right) ChIP-Seq binding profile for H3K27ac at the IL2RA locus in Th cells. (FIG. 15C) (top left) Radar plots showing the density of non-coding SNPs linked to systemic lupus erythematosus (SLE) in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types. (top right) Distribution of non-coding SNPs linked to SLE in the typical enhancers and super-enhancers of B cells. (bottom left) List of genes associated with SLE SNP-containing super-enhancers in B cells. (bottom right) ChIP-Seq binding profile for H3K27ac at the HLA DRB1 and HLA-DQA1 loci in B cells.

FIGS. 16(A)-16(E) illustrate super-enhancers in cancer. (FIG. 16A) Selected genes associated with super-enhancers in the indicated cancers. (FIG. 16B) Cancer cells acquire super-enhancers. ChIP-Seq binding profiles for H3K27ac are shown at the gene desert surrounding MYC in pancreatic cancer, T cell leukemia, colorectal cancer, and healthy counterparts. (FIG. 16C) Chromosomal translocation, overexpression of transcription factors and focal amplification may contribute to super-enhancer formation in cancer. (FIG. 16D) Tumor-specific super-enhancers associate with hallmark cancer genes in colorectal cancer. (FIG. 16E) Super-enhancers acquired by cancer cells associate with hallmark genes.

FIGS. 17(A)-17(C) show genomic localization and features of transcription factors in mESCs. (FIG. 17A) Metagene representations of mean ChIP-Seq density in regions surrounding constituents of super-enhancers and typical enhancers, active promoters, and the borders of topological domains for the indicated transcription factors in mESCs. (FIG. 17B) (top) Table depicting transcription factor binding motifs at constituent enhancers within typical enhancer regions, and associated p-values. (FIG. 17C) Comparison of motif frequency per constituent of super-enhancers and typical enhancers shows that super-enhancer constituents are enriched in motif occurrences for these factors compared to typical enhancer constituents (t test, p<10⁻¹⁵).

FIGS. 18(A)-18(C) show that super-enhancer-associated genes are especially sensitive to perturbation. (FIG. 18A) (top) Schematic diagram the shRNAs knockdown of Oct4 in mESCs. (bottom) Box plots of fold change expression for all enhancer-associated genes, typical enhancer-associated genes and super-enhancer-associated genes 3, 4 and 5 days after knockdown. (FIG. 18B) (top) Schematic diagram the shRNAs knockdown of the Mediator subunit Med12 in mESCs. (bottom) Box plots of fold change expression for all enhancer-associated genes, typical enhancer-associated genes and super-enhancer-associated genes 3, 4 and 5 days after knockdown. (FIG. 18C) (top) Schematic diagram the shRNAs knockdown of the cohesin subunit Smc1 in mESCs. (bottom) Box plots of fold change expression for all enhancer-associated genes, typical enhancer-associated genes and super-enhancer-associated genes 3, 4 and 5 days after knockdown.

FIGS. 19(A)-19(D) show the identification and characterization of super-enhancers using H3K27ac. (FIG. 19A) Comparison of the abilities of enhancer surrogate marks (p300, H3K27ac, H3K4me1, DNase hypersensitivity) to identify super-enhancers and super-enhancer-associated genes in mESCs. (FIG. 19B) Heatmap showing the classification of super-enhancer-associated genes across 26 human cell and tissue types. (FIG. 19C) Heatmap showing the classification of typical enhancer-associated genes across 26 human cell and tissue types. (FIG. 19D) Super-enhancers can overlap with Locus Control Regions (LCR), Transcription Initiation Platforms (TIP) and DNA methylation valleys (DMV).

FIGS. 20(A)-20(C) show disease-associated sequence variation is enriched in super-enhancers. (FIG. 20A) Summary of trait-associated SNPs in the union of super-enhancers, typical enhancers and regulatory regions (defined as H3K27ac binding peaks) in 86 human cell and tissue samples. (FIG. 20B) The SNP enrichment values of non-coding SNPs linked to the highlighted traits and diseases in the union of super-enhancers, typical enhancers and regulatory regions (defined as H3K27ac binding peaks) in 86 human cell and tissue samples. (FIG. 20C) Radar plots showing the density of non-coding SNPs linked to selected diseases in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types.

FIG. 21 shows super-enhancers around the MYC locus. ChIP-Seq binding profiles for H3K27ac at the c-MYC locus in the indicated cancer samples.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates in some aspects to super-enhancers and related compositions, methods, and agents that are useful for modulating expression of cell type-specific genes that are required for maintenance of cell identity (e.g., embryonic stem cell identity) or maintenance of a disease state (e.g., cancer). In some aspects, the present invention relates to methods of identifying super-enhancers, super-enhancer-associated genes, and disease-related genes in cells, tissues, organs and individuals, and kits comprising reagents for performing those methods.

During the course of work described herein, more than 200 genomic regions that contained tightly spaced clusters of enhancers spanning extraordinarily large domains were discovered. These “super-enhancers” are occupied by more transcriptional coactivator (e.g., Mediator) than the average or median enhancers, exhibit greater activity than average enhancers, and are sufficient to drive high expression of key, cell type-specific genes required to maintain cell identity or disease state.

Accordingly, in some aspects, the present invention relates to an isolated super-enhancer, or functional fragment and/or variant thereof, comprising a genomic region of DNA that contains at least two enhancers, wherein the genomic region is occupied when present within a cell by more super-enhancer component, e.g., transcriptional coactivator or RNA such as eRNA, than the average single enhancer within the cell. As used herein, “enhancer” refers to a short region of DNA to which proteins (e.g., transcription factors) bind to enhance transcription of a gene. As used herein, “transcriptional coactivator” refers to a protein or complex of proteins that interacts with transcription factors to stimulate transcription of a gene. In some embodiments, the transcriptional coactivator is Mediator. In some embodiments, the transcriptional coactivator is Med1 (Gene ID: 5469). In some embodiments, the transcriptional coactivator is a Mediator component. As used herein, “Mediator component” comprises or consists of a polypeptide whose amino acid sequence is identical to the amino acid sequence of a naturally occurring Mediator complex polypeptide. The naturally occurring Mediator complex polypeptide can be, e.g., any of the approximately 30 polypeptides found in a Mediator complex that occurs in a cell or is purified from a cell (see, e.g., Conaway et al., 2005; Kornberg, 2005; Malik and Roeder, 2005). In some embodiments a naturally occurring Mediator component is any of Med1-Med 31 or any naturally occurring Mediator polypeptide known in the art. For example, a naturally occurring Mediator complex polypeptide can be Med6, Med7, Med10, Med12, Med14, Med15, Med17, Med21, Med24, Med27, Med28 or Med30. In some embodiments a Mediator polypeptide is a subunit found in a Med11, Med17, Med20, Med22, Med 8, Med 18, Med 19, Med 6, Med 30, Med 21, Med 4, Med 7, Med 31, Med 10, Med 1, Med 27, Med 26, Med14, Med15 complex. In some embodiments a Mediator polypeptide is a subunit found in a Med12/Med13/CDK8/cyclin complex. Mediator is described in further detail in PCT International Application No. WO 2011/100374, the teachings of which are incorporated herein by reference in their entirety. In some embodiments, Mediator occupation of an enhancer, e.g., a superenhancer, may be detected by detecting one or more Mediator components. It is to be understood that a Mediator inhibitor may inhibit one or more Mediator components or inhibit interaction(s) between them or inhibit interaction with a transcription factor.

In some embodiments a “naturally occurring polypeptide” is a polypeptide that naturally occurs in a eukaryote, e.g., a vertebrate, e.g., a mammal. In some embodiments the mammal is a human. In some embodiments the vertebrate is a non-human vertebrate, e.g., a non-human mammal, e.g., rodent, e.g., a mouse, rat, or rabbit. In some embodiments the vertebrate is a fish, e.g., a zebrafish. In some embodiments the eukaryote is a fungus, e.g., a yeast. In some embodiments the eukaryote is an invertebrate, e.g., an insect, e.g., a Drosophila, or a nematode, e.g., C. elegans. Any eukaryotic species is encompassed in various embodiments of the invention. Similarly a cell, tissue, or subject can be of any eukaryotic species in various embodiments of the invention. In some embodiments, the sequence of the naturally occurring polypeptide is the sequence most commonly found in the members of a particular species of interest. One of skill in the art can readily obtain sequences of naturally occurring polypeptides, e.g., from publicly available databases such as those available at the National Center for Biotechnology Information (NCBI) website (e.g., GenBank, OMIM, Gene).

In some embodiments, the transcriptional coactivator is a component of Mediator. In some embodiments, the Mediator component comprises a Med1 or a Med12 polypeptide. In some embodiments, the at least one Mediator component comprises Med6, Med7, Med10, Med12, Med14, Med15, Med17, Med21, Med24, Med27, Med28 and Med30 polypeptides.

In some embodiments, the genomic region of the super-enhancer is occupied when present within a cell by more chromatin regulator than the average single enhancer within the cell. As used herein, “chromatin regulator” refers to a protein or complex of proteins that is involved in regulating gene expression by interacting with transcription factors, transcriptional coactivators, and/or acetylated histone residues in a way that modulates expression of a super-enhancer-associated gene. In some instances, the chromatin regulator possesses histone acetyltransferase (HAT) activity. HATs are responsible for acetylating lysine residues on histone tails of nucleosomes, thereby relaxing the chromatin and increasing access to DNA. In some embodiments, the chromatin regulator is a BET bromodomain protein. In some embodiments, the BET bromodomain protein is BRD4 (Gene ID: 23476).

In some embodiments, the genomic region of the super-enhancer is occupied when present within a cell by more RNA, e.g., enhancer RNA (eRNA), than the average single enhancer within the cell. As used herein, enhancer RNA (eRNA) refers to a class of relatively short non-coding RNA molecules (50-2000 nucleotides) transcribed from the DNA sequence of an enhancer region, such as a super-enhancer.

Generally, super-enhancers formed by the at least two enhancers in the genomic region of DNA are of greater length than the average single enhancer. In some embodiments, the length of the genomic region that forms the super-enhancer is at least an order of magnitude greater than the average single enhancer. In some embodiments the genomic region spans between about 4 kilobases and about 500 kilobases in length. In some embodiments, the genomic region spans between about 4 kilobases and about 40 kilobases in length. It should be appreciated, however, that super-enhancers may comprise genomic regions less than 4 kilobases or greater than 40 kilobases in length, as long as the genomic region contains clusters of enhancers that can be occupied when present within a cell by extremely high levels of a transcriptional coactivator (e.g., Mediator).

The tables disclosed herein, for example, Table 1 (relating to nucleotide sequences of super-enhancers found within embryonic stem cells) and Table 2 (relating to nucleotide sequences of super-enhancers found within multiple myeloma cells); Table 3 (relating to nucleotide sequences of super-enhancers found in glioblastoma cells); and Table 4 (relating to nucleotide sequences of super-enhancers found in SCLC cells) disclose information that can be relied upon by one of skill in the art to obtain the specific nucleotide sequences for exemplary super-enhancers of the invention. For example, using the chromosomal number, and start and stop positions, as well as the sense orientation (e.g. +) of the sequence provided in Tables 1 and 2, one of skill in the art would be able to utilize a publicly available database (e.g., USCS Genome Browser, available at genome.ucsc.edu/) to obtain the nucleotide sequences of the specified super-enhancers. For the embryonic stem cell super-enhancer nucleotide sequences specified in Table 1, the mm9 genome build was used. This corresponds to NCBI build 37. For the multiple myeloma cell super-enhancer nucleotide sequences specified in Table 2, the hg 18 genome build was used. This corresponds to NCBI build 36. Tables 3 and 4 are also based on the hg 18 genome build. In some embodiments, the invention comprises a super-enhancer, or functional fragment and/or variant thereof, having a nucleotide sequence specified in a table described herein, e.g., any of Tables 1-90.

The at least two enhancers which form the super-enhancers, or functional fragment and/or variant thereof, are clustered together.

It should be appreciated that the each of the at least two enhancers can be the same type of enhancer or the at least two enhancers can be different types of enhancers. Each enhancer of the at least two enhancers comprises a binding site for a cognate transcription factor that interacts with the transcriptional coactivator to stimulate transcription of the gene associated with the super-enhancer. In some embodiments, the cognate transcription factor comprises an embryonic stem cell master transcription factor. Examples of suitable embryonic stem cell master transcription factors include, but are not limited to Oct4, Sox2, Nanog, Esrrb, Utf1, K1f4, mir-290-295 gene cluster, Tbx3, Sgk1, and combinations thereof. In some embodiments, the embryonic stem cell master transcription factor is one or more of Nr5a2, Prdm14, Tcfcp211, Smad3, Stat3 or Tcf3. In some embodiments, the embryonic stem cell master transcription factor Oct 4, Sox2, Nanog, K1f4, Esrrb, Nr5a2, Prdm14, Tcfcp211, Smad3, Stat3 or Tcf3. In some embodiments, the transcription factor is directly down to its known DNA sequence motif.

In some embodiments, the cognate transcription factor comprises an oncogenic transcription factor. Examples of suitable oncogenic transcription factors include, but are not limited to c-Myc, IRF4, p53, AP-1, Bcr-Abl, c-Fos, c-Jun and combinations thereof. In some embodiments, the cognate transcription factor comprises a muscle cell transcription factor, for example, transcription factor MyoD. In some embodiments, the cognate transcription factor comprises a B cell transcription factor, for example Pu.1.

In some embodiments, the cognate transcription factor comprises a transcription factor of a gene associated with a hallmark of a disease such as cancer, e.g., cancer of cells or tissues disclosed herein. In some embodiments, the cognate transcription factor comprises a transcription factor of a gene having a disease associated DNA sequence variation such as a SNP, e.g., in cells or tissues disclosed herein. In some embodiments, the disease is Alzheimer's disease, and the gene is BIN1 (e.g., having a disease associated DNA sequence variation such as a SNP). In some embodiments, the disease is type 1 diabetes, and the gene is associated with a primary Th cell (e.g., having a disease associated DNA sequence variation such as a SNP). In some embodiments, the disease is systemic lupus erythematosus, and the gene plays a key role in B cell biology (e.g., having a disease associated DNA sequence variation such as a SNP).

In some embodiments, the gene comprises a disease-associated variation related to rheumatoid arthritis, multiple sclerosis, systemic scleroderma, primary biliary cirrhosis, Crohn's disease, Graves disease, vitiligo and atrial fibrillation.

As noted above, the genomic region of the super-enhancers are occupied when present within a cell by more transcriptional coactivator (e.g., Mediator), more chromatin regulator (e.g., BRD4), and/or more RNA (e.g., eRNA) than the average single enhancer within the cell. In some embodiments, the genomic region of a super-enhancers is occupied when present within the cell by an order of magnitude more transcriptional coactivator, chromatin regulator, or RNA than the average single enhancer in the cell. As used herein, “order of magnitude” refers to the relative fold difference in a feature or classification of one object as compared to a feature or classification of another object (e.g., a level or an amount of transcriptional coactivator occupying a super-enhancer associated with a gene as compared to the level or the amount of transcriptional coactivator occupying the average or median enhancer associated with the gene). In some embodiments, the order of magnitude is at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold or more. In some embodiments, the order of magnitude is at least 2-fold (i.e., there is a 2-fold greater amount of transcriptional coactivator occupying the super-enhancer associated with a gene than the amount of transcriptional coactivator occupying the average enhancer in the gene). In some embodiments, the order of magnitude is at least 10-fold. In some embodiments, the order of magnitude is at least 15-fold. In some embodiments, the order of magnitude is at least 16-fold.

Work described herein suggests that super-enhancers are a common feature of mammalian cells. Accordingly, the present invention contemplates that super-enhancers can be isolated from any mammalian cell type. Such isolation can be achieved by routine methods well known to those skilled in the art. Exemplary cells and tissues that include superenhancer are human cells; fetal cells; embryonic stem cells or embryonic stem cell-like cells, e.g., cells from the umbilical vein, e.g., endothelial cells from the umbilical vein; muscle, e.g., myotube, fetal muscle; blood cells, e.g., cancerous blood cells, fetal blood cells, monocytes; B cells, e.g., Pro-B cells; brain, e.g., astrocyte cells, angular gyms of the brain, anterior caudate of the brain, cingulate gyms of the brain, hippocampus of the brain, inferior temporal lobe of the brain, middle frontal lobe of the brain, brain cancer cells; T cells, e.g., naïve T cells, memory T cells; CD4 positive cells; CD25 positive cells; CD45RA positive cells; CD45RO positive cells; IL-17 positive cells; cells stimulated with PMA; Th cells; Th17 cells; CD255 positive cells; CD127 positive cells; CD8 positive cells; CD34 positive cells; duodenum, e.g., smooth muscle tissue of the duodenum; skeletal muscle tissue; myoblast; stomach, e.g., smooth muscle tissue of the stomach, e.g., gastric cells; CD3 positive cells; CD14 positive cells; CD19 positive cells; CD20 positive cells; CD34 positive cells; CD56 positive cells; prostate, e.g., prostate cancer; colon, e.g., colorectal cancer cells; crypt cells, e.g., colon crypt cells; intestine, e.g., large intestine; e.g., fetal intestine; bone, e.g., osteoblast; pancreas, e.g., pancreatic cancer; adipose tissue; adrenal gland; bladder; esophagus; heart, e.g., left ventricle, right ventricle, left atrium, right atrium, aorta; lung, e.g., lung cancer cells; skin, e.g., fibroblast cells; ovary; psoas muscle; sigmoid colon; small intestine; spleen; thymus, e.g., fetal thymus; breast, e.g., breast cancer; cervix, e.g., cervical cancer; mammary epithelium; liver, e.g., liver cancer; DND41 cells; GM12878 cells; H1 cells; H2171 cells; HCC1954 cells; HCT-116 cells; HeLa cells; HepG2 cells; HMEC cells; HSMM tube cells; HUVEC cells; IMR90 cells; Jurkat cells; K562 cells; LNCaP cells; MCF-7 cells; MM1S cells; NHLF cells; NHDF-Ad cells; RPMI-8402 cells; U87 cells; VACO 9M cells; VACO 400 cells; and VACO 503 cells.

In some embodiments, super-enhancers of the present invention can be used drive high levels of expression of cell type specific genes. A cell type specific gene is typically expressed selectively in one or a small number of cells types relative to expression in many or most other cell types. One of skill in the art will be aware of numerous genes that are considered cell type specific. A cell type specific gene need not be expressed only in a single cell type but may be expressed in one or several, e.g., up to about 5, or about 10 different cell types out of the approximately 200 commonly recognized (e.g., in standard histology textbooks) and/or most abundant cell types in an adult vertebrate, e.g., mammal, e.g., human. In some embodiments, a cell type specific gene is one whose expression level can be used to distinguish a cell, e.g., a cell as disclosed herein, such as a cell of one of the following types from cells of the other cell types: adipocyte (e.g., white fat cell or brown fat cell), cardiac myocyte, chondrocyte, endothelial cell, exocrine gland cell, fibroblast, glial cell, hepatocyte, keratinocyte, macrophage, monocyte, melanocyte, neuron, neutrophil, osteoblast, osteoclast, pancreatic islet cell (e.g., a beta cell), skeletal myocyte, smooth muscle cell, B cell, plasma cell, T cell (e.g., regulatory, cytotoxic, helper), or dendritic cell. In some embodiments a cell type specific gene is lineage specific, e.g., it is specific to a particular lineage (e.g., hematopoietic, neural, muscle, etc.) In some embodiments, a cell-type specific gene is a gene that is more highly expressed in a given cell type than in most (e.g., at least 80%, at least 90%) or all other cell types. Thus specificity may relate to level of expression, e.g., a gene that is widely expressed at low levels but is highly expressed in certain cell types could be considered cell type specific to those cell types in which it is highly expressed. It will be understood that expression can be normalized based on total mRNA expression (optionally including miRNA transcripts, long non-coding RNA transcripts, and/or other RNA transcripts) and/or based on expression of a housekeeping gene in a cell. In some embodiments, a gene is considered cell type specific for a particular cell type if it is expressed at levels at least 2, 5, or at least 10-fold greater in that cell than it is, on average, in at least 25%, at least 50%, at least 75%, at least 90% or more of the cell types of an adult of that species, or in a representative set of cell types. One of skill in the art will be aware of databases containing expression data for various cell types, which may be used to select cell type specific genes. In some embodiments a cell type specific gene is a transcription factor.

In some aspects, the present invention relates to a composition comprising a super-enhancer of the present invention or a functional variant thereof. Such compositions may be useful for stimulating the expression of a gene or genes in a specific cell type, for example, to stimulate the expression of embryonic stem cell master transcription factors to maintain the cell in an embryonic stem cell-like state. In some instances, such compositions may be useful for stimulating the expression of a gene or genes in a specific cell type to change the identity of a specific cell-type, for example, by introducing a super-enhancer associated with a differentiated state to change the identity of an embryonic stem cell to a more differentiated state. In some embodiments, the super-enhancer can be used to stimulate expression of a target gene that is to be transfected into a cell for in vitro expression of that target gene. In some embodiments, the super-enhancer can be used to simulate a disease like state. By way of example, and not of limitation, a super-enhancer can be constructed using enhancers of an oncogene and transfection of the oncogene with the artificial enhancer can be useful to simulate the disease associated with the oncogene. Another exemplary use of a super-enhancer of the present invention is to identify genes including, for example, a gene having disease-associated DNA sequence variation such as a SNP, that are prone to lead to disease upon aberrant expression. Such super-enhancers may be used in cells, tissues, organs, and whole organisms to artificially increase the expression of certain genes and examine the biological effects that the increased expression of the gene has on the cell, the tissue, organ, or animal.

It should be appreciated that any enhancer associated with the target gene can be cloned and used to form the super-enhancers. In some embodiments, the super-enhancer is engineered to mimic a super-enhancer identified in vivo, such as a super-enhancer that is responsible for maintaining embryonic stem cell identity, i.e., a super-enhancer comprising a plurality of Oct4, Sox2, and Nanog binding motifs oligomerized to form a concatemer.

In some aspects, the present invention relates to a nucleic acid construct comprising a super-enhancer, or functional fragment thereof, of the present invention. Methods of forming nucleic acid constructs are known to those skilled in the art. It should be understood that the nucleic acid constructs of the present invention are artificial or engineered constructs not to be confused with native genomic sequences. Such nucleic acid constructs can be used, for example, to increase the expression of a gene or genes associated with or regulated by the super-enhancer in the nucleic acid construct. In some instances, a nucleic acid construct comprising the super-enhancer can be introduced into a target cell and the super-enhancer can interact with endogenous cellular components to drive expression of an endogenous gene within the cell. In some embodiments, the nucleic acid construct includes a nucleotide sequence encoding a target gene operatively linked to the super-enhancer. In such instances, the nucleic acid can be transfected into a cell and interact with endogenous cellular components to drive expression of the exogenous target gene associated with the super-enhancer. In other embodiments, the nucleic acid construct can include a nucleic acid sequence encoding a transcriptional coactivator or chromatin regulator that can be expressed within the cell to produce transcriptional coactivator or chromatin regulator that can occupy the genomic region of the super-enhancer and increase expression of the gene associated with the super-enhancer in the cell. In some embodiments, the nucleic acid can include a reporter.

In some embodiments a reporter comprises a nucleic acid sequence that encodes a detectable marker, e.g., a fluorescent protein such as green fluorescent protein (GFP), blue, sapphire, yellow, red, orange, and cyan fluorescent proteins and fluorescent variants such as enhanced GFP (eGFP), mFruits such as mCherry, mTomato, mStrawberry; R-Phycoerythrin, etc. Enzymes useful as reporters include, e.g., enzymes that act on a substrate to produce a colored, fluorescent, or luminescent substance. Examples include luciferases, beta-galactosidase, horseradish peroxidase, and alkaline phosphatase. In some embodiments, alteration (e.g., reduction) in the level of a reporter may be used to identify a compound that modulates (e.g., inhibits) activity of a super-enhancer.

In some aspects, the present invention relates to a kit for increasing the expression of a gene, the kit including one or more or all of: (a) a population of cells; (b) reagents suitable for culturing said population of cells; (c) a nucleic acid construct comprising a super-enhancer enhancer or functional fragment and/or variant thereof, and a gene associated with the super-enhancer enhancer or functional fragment and/or variant thereof, that is capable of being expressed within said population of cells; and optionally (d) transcriptional coactivator, chromatin regulator, or RNA e.g., excess levels of transcriptional coactivator, chromatin regulator, or RNA that, e.g., can be introduced into said population of cells such that an order of magnitude more transcriptional coactivator, chromatin, or RNA regulator occupies enhancers clustered within the super-enhancer and increases the expression of the gene within the cells.

In some aspects, the present invention relates to a cell, or cell-free system, into which a super-enhancer is introduced, for example by transfection of a nucleic acid construct comprising the super-enhancer, wherein upon introduction of super-enhancer into the cell, or cell-free system, endogenous transcriptional coactivators and chromatin regulators within the cell co-occupy the enhancer clusters of the super-enhancer and the active transcription start sites of the target gene to stimulate expression of the target gene within the cell. It should be appreciated that the super enhancer, or functional fragment and/or variant thereof, may be associated with and regulate an endogenous gene within the transfected cell. In such instances, the gene regulated by the super-enhancer, or functional fragment and/or variant thereof, need not be introduced into the cell with the super-enhancer, for example a nucleic acid construct need not include a target gene for expression within the transfected cell. In other instances, such as when an exogenous gene is desired to be introduced within the transfected cell, or cell-free system, the exogenous gene can be introduced into the cell with the super-enhancer, or functional fragment and/or variant thereof, or functional fragment and/or variant thereof. It should be appreciated that the exogenous gene and the super-enhancer or functional fragment and/or variant thereof, can be introduced into the cell by any method and in any form (e.g., protein or nucleic acid). The exogenous gene and the super-enhancer, or functional fragment and/or variant thereof, can be introduced into the cell, or cell-free system, together or separately, for example a nucleic acid construct comprising the super enhancer, or functional fragment and/or variant thereof, may be further engineered to include an exogenous gene operatively linked to the super-enhancer, or functional fragment and/or variant thereof, and which is also capable of being expressed within the transfected cell, or cell-free system. In some embodiments, exogenous transcriptional coactivators and/or chromatin regulators can be introduced into the transfected cell, or cell-free system to ensure that the enhancer clusters of the super-enhancer and the active transcription start sites are co-occupied within the transfected cell, or cell-free system by more transcriptional coactivator and/or the chromatin regulator and thereby drive high levels of expression of either an exogenous or endogenous gene in the transfected cell, or cell-free system.

The super-enhancer and/or a nucleic acid construct comprising the super-enhancer, or functional fragment and/or variant thereof, can be transfected into any cell suitable for expressing the gene associated with the super-enhancer. In some embodiments, the cell is a mammalian cell. In some embodiments, the cell is a human cell. In some embodiments, the cell is an embryonic stem cell or embryonic stem cell-like cell. In some embodiments, the cell is a muscle cell. In some embodiments, the muscle cell is a myotube. In some embodiments, the cell is a B cell. In some embodiments, the B cell is a Pro-B cell. Additional exemplary cells and tissues include: fetal cells; cells from the umbilical vein, e.g., endothelial cells from the umbilical vein; muscle, e.g., fetal muscle; blood cells, e.g., cancerous blood cells, fetal blood cells, monocytes; brain, e.g., astrocyte cells, angular gyms of the brain, anterior caudate of the brain, cingulate gyms of the brain, hippocampus of the brain, inferior temporal lobe of the brain, middle frontal lobe of the brain, brain cancer cells; T cells, e.g., naïve T cells, memory T cells; CD4 positive cells; CD25 positive cells; CD45RA positive cells; CD45RO positive cells; IL-17 positive cells; cells stimulated with PMA; Th cells; Th17 cells; CD255 positive cells; CD127 positive cells; CD8 positive cells; CD34 positive cells; duodenum, e.g., smooth muscle tissue of the duodenum; skeletal muscle tissue; myoblast; stomach, e.g., smooth muscle tissue of the stomach, e.g., gastric cells; CD3 positive cells; CD14 positive cells; CD19 positive cells; CD20 positive cells; CD34 positive cells; CD56 positive cells; prostate, e.g., prostate cancer; colon, e.g., colorectal cancer cells; crypt cells, e.g., colon crypt cells; intestine, e.g., large intestine; e.g., fetal intestine; bone, e.g., osteoblast; pancreas, e.g., pancreatic cancer; adipose tissue; adrenal gland; bladder; esophagus; heart, e.g., left ventricle, right ventricle, left atrium, right atrium, aorta; lung, e.g., lung cancer cells; skin, e.g., fibroblast cells; ovary; psoas muscle; sigmoid colon; small intestine; spleen; thymus, e.g., fetal thymus; breast, e.g., breast cancer; cervix, e.g., cervical cancer; mammary epithelium; liver, e.g., liver cancer; DND41 cells; GM12878 cells; H1 cells; H2171 cells; HCC1954 cells; HCT-116 cells; HeLa cells; HepG2 cells; HMEC cells; HSMM tube cells; HUVEC cells; IMR90 cells; Jurkat cells; K562 cells; LNCaP cells; MCF-7 cells; MM1S cells; NHLF cells; NHDF-Ad cells; RPMI-8402 cells; U87 cells; VACO 9M cells; VACO 400 cells; and VACO 503 cells.

In some aspects, the present invention relates to a functional variant of a super-enhancer. A variant may be shorter or longer than the original super-enhancer. The term “variant” encompasses “fragments” or “functional fragments” of super-enhancers, or functional sequence variants, of super-enhancers. A “fragment” is a continuous portion of a polypeptide or polynucleotide that is shorter than the original polypeptide or polynucleotide. In some embodiments a variant comprises or consists of a fragment. In some embodiments a fragment or variant is at least 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or more as long as the original polypeptide or polynucleotide. A fragment may be an N-terminal, C-terminal, or internal fragment. A functional fragment of a super-enhancer can have one or more of the following properties:

a) when associated with a gene, e.g., a gene with which it is normally associated, it provides at least 10, 20, 30, 40, 50, 60, 70, 80, or 90% of the level of expression as is seen with the intact super-enhancer;

b) when associated with a gene, e.g., a gene with which it is normally associated, it provides at least 10, 20, 30, 40, 50, 60, 70, 80, or 90% of the level of binding of an super-enhancer component;

c) when associated with a gene, e.g., a gene with which it is normally associated, it provides at least 10, 20, 30, 40, 50, 60, 70, 80, or 90% of the level of binding of a mediator protein, e.g., Med1;

d) it comprises at least 10, 20, 30, 40, 5, 60, 70, 80 or 90% of the enhancers of the super-enhancer of which it is a functional fragment;

e) it is at least 10, 20, 30, 40, 5, 60, 70, 80 or 90% as long as the super-enhancer of which it is a functional fragment.

The term variant also encompasses “sequence variants,” e.g., “functional sequence variants,” of a super enhancer or fragment or functional fragment of a super-enhancer. A functional sequence variant of a super-enhancer can have one or more of the following properties:

a) it comprises sufficient nucleotide sequence homology or identity with a reference super-enhancer, e.g., the super-enhancer from which it is derived, that when associated with a gene, e.g., a gene with which the reference super-enhancer is normally associated, it provides at least 10, 20, 30, 40, 50, 60, 70, 80, or 90% of the level of expression as is seen with the reference super-enhancer;

b) when associated with a gene, e.g., a gene with which the reference super-enhancer, e.g., the super-enhancer from which it is derived, is normally associated, it provides at least 10, 20, 30, 40, 50, 60, 70, 80, or 90% of the level of binding of an super-enhancer component as is seen with the reference super-enhancer;

c) when associated with a gene, e.g., a gene with which the reference super-enhancer, e.g., the super-enhancer from which it is derived, is normally associated, it provides at least 10, 20, 30, 40, 50, 60, 70, 80, or 90% of the level of binding of a mediator protein, e.g., Med1 as is seen with the reference super-enhancer;

d) it comprises at least 10, 20, 30, 40, 5, 60, 70, 80 or 90% of the number of functional enhancers as is seen with the reference super-enhancer, e.g., the super-enhancer from which it is derived;

e) it comprises at least 40, 50, 60, 70, 80, 90, 95, 97, or 99% sequence homology or identity with a reference super-enhancer, e.g., the super-enhancer from which it is derived;

f) it comprises at least 40, 50, 60, 70, 80, 90, 95, 97, or 99% sequence homology or identity, across its encompassed enhancer elements, with a reference super-enhancer, e.g., the super-enhancer from which it is derived; or

f) it comprises a first level or sequence or homology or identity across its encompassed enhancer elements and/or associated protein encoding element, and a second level of homology across untranslated and/or untranscribed regions between its encompassed enhancers, with a reference super-enhancer, e.g., the super-enhancer from which it is derived, wherein the first and second levels are independently selected from at least 40, 50, 60, 70, 80, 90, 95, 97, or 99% sequence homology or identity, and, e.g., the first level is higher than the second level, e.g., the first level is at least 80, 90, 95, 97, or 99% and the second level is at least 40, 50, or 60%.

In some embodiments a variant polypeptide comprises or consists of at least one domain of an original polypeptide. In some embodiments a variant polynucleotide hybridizes to an original polynucleotide under stringent conditions, e.g., high stringency conditions, for sequences of the length of the original polypeptide. In some embodiments a variant polypeptide or polynucleotide comprises or consists of a polypeptide or polynucleotide that is at least 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or more identical in sequence to the original polypeptide or polynucleotide over at least 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of the original polypeptide or polynucleotide. In some embodiments a variant polypeptide comprises or consists of a polypeptide that is at least 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or more identical in sequence to the original polypeptide over at least 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of the original polypeptide, with the proviso that, for purposes of computing percent identity, a conservative amino acid substitution is considered identical to the amino acid it replaces. In some embodiments a variant polypeptide comprises or consists of a polypeptide that is at least 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or more identical to the original polypeptide over at least 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% of the original polypeptide, with the proviso that any one or more amino acid substitutions (up to the total number of such substitutions) may be restricted to conservative substitutions. In some embodiments a percent identity is measured over at least 100; 200; 300; 400; 500; 600; 700; 800; 900; 1,000; 1,200; 1,500; 2,000; 2,500; 3,000; 3,500; 4,000; 4,500; or 5,000 amino acids. In some embodiments the sequence of a variant polypeptide comprises or consists of a sequence that has N amino acid differences with respect to an original sequence, wherein N is any integer between 1 and 10 or between 1 and 20 or any integer up to 1%, 2%, 5%, or 10% of the number of amino acids in the original polypeptide, where an “amino acid difference” refers to a substitution, insertion, or deletion of an amino acid. In some embodiments a difference is a conservative substitution. Conservative substitutions may be made, e.g., on the basis of similarity in side chain size, polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues involved. In some embodiments, conservative substitutions may be made according to Table A, wherein amino acids in the same block in the second column and in the same line in the third column may be substituted for one another other in a conservative substitution. Certain conservative substitutions are substituting an amino acid in one row of the third column corresponding to a block in the second column with an amino acid from another row of the third column within the same block in the second column.

TABLE A Aliphatic Non-polar G A P I L V Polar - uncharged C S T M N Q Polar - charged D E K R Aromatic H F W Y

In some aspects, the present invention relates to a method of increasing the level of expression of a target gene in a cell, the method including transfecting a cell under conditions suitable for expression of the target gene with a nucleic acid expression construct comprising a nucleic acid sequence encoding the target gene operatively linked to a super-enhancer, wherein upon transfection of the cell endogenous transcriptional coactivators and chromatin regulators within the cell co-occupy enhancers clustered within the super-enhancer and active transcription start sites of the target gene to increase the level of expression of the target gene within the cell. Those skilled in the art will appreciate that the step of transfecting can be achieved in a variety of ways according to well-known and routine methods, for example, by using a transfection reagent, such as a plasmid or a lipid based transfection reagent. In some instances, it may be desirable to introduce into the cell exogenous transcriptional coactivators and chromatin regulators to ensure that enhancers clustered within the super-enhancer and the activate transcription start sites of the target gene are co-occupied by an order of magnitude more of the transcriptional coactivators and chromatin regulators than the average enhancer of the target gene. The exogenous transcriptional coactivators and chromatin regulators can be introduced into the target cell in the form of nucleic acids that can be transfected into the cell for expression within the cell or in the form of proteins, for example, by microinjecting the proteins into the cell. Other ways of introducing nucleic acids and proteins into a cell are apparent to those skilled in the art. Upon transfection of the cell with the nucleic acid construct containing the super enhancer, or functional fragment and/or variant thereof, it is expected that the level of expression of the target gene will increase significantly, for example, the level of expression of the target gene is increased 2-fold, 3-fold, 4-fold, 5-fold, 6-fold or more within the cell.

In some aspects, the present invention relates to a kit for increasing the expression of a target gene in a cell, comprising one or more or all of: (a) a super-enhancer operatively linked to a target gene; (b) a population of cells suitable for expression of said target gene; and (c) a reagent for introducing the super-enhancer and the target gene into said population of cells. In some embodiments, the reagent comprises a transfection reagent, e.g., a plasmid.

In some aspects, the present invention relates to a kit for increasing the expression of a target gene in a cell, comprising one or more or all of: (a) a nucleic acid construct comprising an artificial super-enhancer operatively linked to the target gene; (b) a population of cells suitable for expression of said target gene; and (c) a reagent for transfecting said population of cells with said nucleic acid construct.

In some aspects, the invention relates to a nucleic acid vector comprising a super-enhancer, or functional fragment and/or variant thereof, and a site, e.g., a restriction enzyme site, disposed such that insertion of a structural gene at the site places the structural gene under the control of the super-enhancer, or functional fragment and/or variant thereof. In embodiments the vector further comprise one or more of a first selectable marker, a second selectable marker, and an origin of replication.

In some aspects, the invention relates to a nucleic acid vector comprising a super-enhancer or functional fragment and/or variant thereof, functionally linked to a heterologous reporter gene, e.g., a fluorescent protein e.g., GFP, or an enzyme, e.g., horse radish peroxidase. In embodiments the vector further comprise one or more of a first selectable marker, a second selectable marker, and an origin of replication.

In some aspects, the invention relates to a kit comprising one or both of:

a first nucleic acid comprising a reference super-enhancer or functional fragment and/or variant thereof, optionally, coupled to a reporter gene; and a second nuclide acid comprising a site for insertion of a super-enhancer, or functional fragment and/or variant thereof, optionally, coupled to a reporter gene.

In some aspects, the invention relates to a kit comprising one or both of:

a nucleic acid vector comprising a super-enhancer, or functional fragment and/or variant thereof, functional linked to a heterologous reporter gene, e.g., a fluorescent protein e.g., GFP, or an enzyme, e.g., horse radish peroxidase. In embodiments the vector further comprise one or more of a first selectable marker, a second selectable marker, and an origin of replication; and

a nucleic acid vector comprising an site, e.g., an restriction enzyme site, and a reporter gene, e.g., a fluorescent protein e.g., GFP, or an enzyme, e.g., horse radish peroxidase, wherein said site is disposed such that insertion into the site of a super-enhancer, or functional fragment and/or variant thereof, will place the reporter gene under the control of the super-enhancer, or functional fragment and/or variant thereof. In embodiments the vector further comprise one or more of a first selectable marker, a second selectable marker, and an origin of replication.

In some aspects, the present invention relates to a method of identifying a super-enhancer in a cell, or cell-free system, comprising: (a) identifying a genomic region of a target gene within said cell, or cell-free system characterized by clusters of enhancers for binding cognate transcription factors capable of interacting with Mediator to stimulate transcription of the target gene within said cell, or cell-free system; (b) measuring in the identified genomic region a level of Mediator occupying said enhancers; and (c) identifying the genomic region as a super-enhancer if the level of Mediator occupying the clusters of enhancers is an order of magnitude more than the level of Mediator occupying the average enhancer of the target gene.

In some aspects, the present invention relates to a method of identifying a super-enhancer in a cell, or cell-free system, comprising: (a) identifying a genomic region of a target gene within said cell, or cell-free system characterized by clusters of enhancers for binding cognate transcription factors capable of interacting with Mediator to stimulate transcription of the target gene within said cell, or cell-free system; (b) measuring in the identified genomic region a level of eRNA associated with the enhancers; and (c) identifying the genomic region as a super-enhancer if the level of eRNA occupying the clusters of enhancers is an order of magnitude more than the level of eRNA occupying the average enhancer of the target gene.

In other aspects, the present invention relates to a method of identifying a super-enhancer associated with a target gene, comprising: (a) analyzing the target gene for a genomic region comprising clusters of enhancers occupied by an order of magnitude more Mediator than an average enhancer of the target gene; and (b) identifying the genomic region as a super-enhancer associated with the target gene if said clusters of enhancers are occupied by the order of magnitude more Mediator than the average enhancer of the target gene In some embodiments, the order of magnitude is at least 2-fold, 10-fold, at least 15-fold, at least 16-fold, or more.

In some aspects, the present invention relates to a method of identifying a gene, e.g., a key gene or genes, that control a cell state or identity, e.g., contributes to unwanted proliferation, e.g., which contributes to a cancerous cell state, comprising: (a) identifying a super-enhancer, e.g., within an animal, cell, or cell-free system; and (b) identifying a gene or genes associated with the super-enhancer, e.g., a gene or genes within a range of proximity to the super-enhancer.

In an embodiment gene or genes that are within a certain proximity to the super-enhancer are identified as a putative key gene or genes that control the cell state or identity. In an embodiment, a gene or genes that are within a certain proximity to the super-enhancer are identified as a hallmark of a disease (e.g., cancer, Alzheimer's, Type 1 diabetes, or Systemic lupus erythematosus). In an embodiment, a gene or genes that are within a certain proximity to the super-enhancer are identified as having a disease associated sequence DNA variation such as a SNP.

In an embodiment the method is performed in a cell-free system.

In an embodiment the method is performed in a cell preparation, e.g., a cultured cell preparation.

In an embodiment the method is performed in an animal model.

In an embodiment the method is first performed in a cell-free system, and repeated in a cell preparation, e.g., a cultured cell preparation.

In an embodiment the method is first performed in a cell-free system, or a cell preparation, e.g., a cultured cell preparation, and repeated in an animal.

In an embodiment the cell is a disease state cell, e.g., a cancer cell.

In an embodiment the cell-free system is derived from a disease state cell, e.g., a cancer cell.

In an embodiment, the identified gene is tested as a target for therapy, e.g., by administering an antagonist or inhibitor, e.g., an siRNA, of the product of the gene, to a cell or animal.

The range of proximity to the super-enhancer can extend as far as about 10 megabases (mb) upstream to one end of the super-enhancer to as far as about 10 mb downstream to the other end of the super-enhancer, and any range therebetween, for example 9 mb upstream to 9 mb downstream, 8 mb upstream to 8 mb downstream, 7 mb upstream to 7 mb downstream, 6 mb upstream to 6 mb downstream, 5 mb upstream to 5 mb downstream, 4 mb upstream to 4 mb downstream, 3 mb upstream to 3 mb downstream, 2 mb upstream to 2 mb downstream to 1 mb upstream to 1 mb downstream, or between 0.5 mb upstream and 0.5 mb downstream, 0.1 mb upstream to 0.1 mb downstream. It should be appreciated that the key genes could also, in some instances, overlap with the super-enhancer region. It is also to be understood that the range of proximity will increase or decrease depending on the length or size of the super-enhancer region, for example, if the super enhancer is 10 kb in length, then the upstream range of proximity extends as far as about 10 mb upstream to the most upstream portion of the 10 kb super-enhancer. Similarly, the downstream range of proximity would extend as far as about 10 mb downstream from the most downstream portion of the 10 kb super-enhancer. In some embodiments, the method of identifying key genes that control the cell state or identity involves measuring the expression of those genes in the cell in the presence and absence of an agent that disrupts the function of the super-enhancer identified, as well as assaying the cell for changes in its cell state or identity (e.g., from a more differentiated state to a less differentiated state, or from a healthy state to a diseased state). If the expression of a gene within the range of proximity is statistically significant when the super-enhancer is properly functioning but its expression decreases or becomes unremarkable in the presence of the agent that disrupts the super-enhancer function, then it is likely that the particular gene is a key gene that controls the cell state or identity, especially if its absence of expression is correlated to a change in the state or identity of the cell.

The aforementioned methods of identifying super-enhancers within a cell and identifying a super-enhancer associated with a target gene can be achieved by a variety of different methods, as would be understood by a person skilled in the art. In some embodiments, the super-enhancer is identified by performing a high throughput sequencing method such as chromatin immunoprecipitation high-throughput sequencing (ChIP-Seq) or RNA-Seq. Example 1 below describes an example of a protocol that can be used to carry out such methods in normal cells, such as embryonic stem cells, for example. Example 2 below describes an example of a protocol that can be used to carry out such methods in tumor cells, such as MM.1S cells, for example.

In certain aspects, the present invention relates to a method of identifying a disease related super-enhancer in a cell, tissue, or organ of an individual suspected of having said disease, comprising: (a) identifying a super-enhancer in said cell, tissue, or organ; (b) identifying a gene associated with said super-enhancer; and (c) and correlating said super-enhancer to said disease.

In an embodiment the disorder is disorder described herein, e.g. a metabolic disorder, e.g., diabetes or obesity, a proliferative disorder, e.g., cancer, or a pre-cancerous disorder, or a neurological disorder, e.g., Alzheimer's disease.

In certain aspects, the present invention relates to a method of characterizing a subject, e.g, a subject having or suspected of having a disorder, e.g., a proliferative disorder, e.g., cancer, comprising:

acquiring a subject tissue sample;

determining if a super-enhancer is associated with a gene, e.g., a preselected gene,

thereby characterizing said subject.

In an embodiment characterizing comprises one or more of diagnosing, prognosing, stratifying or otherwise categorizing the subject.

In an embodiment the sample includes a cell or tissue, e.g., a cell or tissue from any of human cells; fetal cells; embryonic stem cells or embryonic stem cell-like cells, e.g., cells from the umbilical vein, e.g., endothelial cells from the umbilical vein; muscle, e.g., myotube, fetal muscle; blood cells, e.g., cancerous blood cells, fetal blood cells, monocytes; B cells, e.g., Pro-B cells; brain, e.g., astrocyte cells, angular gyms of the brain, anterior caudate of the brain, cingulate gyms of the brain, hippocampus of the brain, inferior temporal lobe of the brain, middle frontal lobe of the brain, brain cancer cells; T cells, e.g., naïve T cells, memory T cells; CD4 positive cells; CD25 positive cells; CD45RA positive cells; CD45RO positive cells; IL-17 positive cells; cells stimulated with PMA; Th cells; Th17 cells; CD255 positive cells; CD127 positive cells; CD8 positive cells; CD34 positive cells; duodenum, e.g., smooth muscle tissue of the duodenum; skeletal muscle tissue; myoblast; stomach, e.g., smooth muscle tissue of the stomach, e.g., gastric cells; CD3 positive cells; CD14 positive cells; CD19 positive cells; CD20 positive cells; CD34 positive cells; CD56 positive cells; prostate, e.g., prostate cancer; colon, e.g., colorectal cancer cells; crypt cells, e.g., colon crypt cells; intestine, e.g., large intestine; e.g., fetal intestine; bone, e.g., osteoblast; pancreas, e.g., pancreatic cancer; adipose tissue; adrenal gland; bladder; esophagus; heart, e.g., left ventricle, right ventricle, left atrium, right atrium, aorta; lung, e.g., lung cancer cells; skin, e.g., fibroblast cells; ovary; psoas muscle; sigmoid colon; small intestine; spleen; thymus, e.g., fetal thymus; breast, e.g., breast cancer; cervix, e.g., cervical cancer; mammary epithelium; liver, e.g., liver cancer.

In an embodiment the determination is memorialized, e.g., in written or in electronic form.

In an embodiment the memorialized determination is transmitted to a recipient, e.g., a health care provider. In an embodiment the memorialization is contained in a report, which can contain other information, e.g., a patient identifier, bibliographic data, e.g. age, gender, race and the like, a description of the subject's condition, suggestions for treatment, or information on the treatment of the subject's disorder.

In an embodiment the method comprises determining the genes in the sample that are associated with a super-enhancer.

In an embodiment, the patient is selected, classified, diagnosed, treated, or prognosed, responsive to the pattern of genes, e.g., a preselected pattern, associated with a super-enhancers, e.g., where a plurality of genes, e.g., a plurality of preselected genes, are associated with super-enhancers.

In an embodiment, the determination comprises: crosslinking chromatin from the sample, and selecting a super-enhancer component, e.g., a target protein, or RNA such as an eRNA.

In an embodiment the target protein is a Mediator protein.

In an embodiment the gene or preselected gene is an oncogene, a kinase, a gene that controls cell proliferation, e.g., a myc gene.

In an embodiment the gene or preselected gene is other than an oncogene, a kinase, a gene that controls cell proliferation, e.g., a myc gene.

In an embodiment the method comprises classifying the subject as having a super-enhancer associated with a gene, e.g., a preselected gene.

In an embodiment the sample comprises cancer cells.

In an embodiment the method comprises characterizing a subject by:

acquiring a subject tissue sample;

determining a gene in the sample is associated with a super-enhancer,

thereby characterizing said subject.

In an embodiment, responsive to said determination, the method comprises selecting and/or administering a therapy to said subject.

In an embodiment, responsive to said determination, the method comprises selecting, classifying, diagnosing, or prognosing said subject.

In an embodiment, responsive to said determination, the method comprises classifying the subject for treatment with an agent that antagonizes or inhibits the product of the gene or preselected gene.

In an embodiment, responsive to said determination, the method comprises administering to the subject an agent that antagonizes or inhibits the product of the gene or preselected gene.

In an embodiment, responsive to said determination, the method comprises administering to the subject an agent that disrupts the super-enhancer associated with the gene (e.g., binds Mediator).

A reaction mixture comprising a patient sample comprising chromatin from a cancer cell and a probe capable of determining if a preselected gene is associated with an super-enhancer. Reaction mixtures described herein are useful, e.g., for determination of the presence of a super-enhancer.

Thus, in another aspect the invention features a reaction mixture which comprises a tissue component, e.g., cells, homogenates, nucleic acid, e.g., chromosomal or mitochondrial DNA, protein, or chromatin. The tissue component can be from a tissue exhibiting, suspected of having, or at risk for having a disorder, e.g., a disorder disclosed herein, e.g., a disorder characterized by unwanted proliferation, e.g., cancer, or a pre-cancerous disorder, inflammatory disorder, neurological disorder, or a metabolic disorder. In an embodiment the tissue component comprises or is from a cancer cell, e.g., a primary or metastatic cancer cell. The tissue component can come from cells of a cancer of described herein (e.g., in a Table described herein, for example, any of Table 1-90). In an embodiment, the probe detects or is selective for a super-enhancer described herein. In an embodiment, the probe detects or is selective for a super-enhancer component associated with a superenhancer described herein, e.g., in one of Tables 1-90.

In embodiments the reaction mixture comprises a probe which can be used to determine if a super-enhancer is present. E.g., the reaction mixture comprises a probe that binds selectively to a super-enhancer component, e.g. binds selectively to a protein, e.g., Med1, H3K27ac, or a transcription factor, or to an eRNA. In embodiments the reaction mixture comprises a reagent capable of cross-linking, e.g., covalently cross-linking, nucleic acid, e.g., chromosomal or mitochondrial DNA, to a super-enhancer component. Exemplary super-enhancer components include a protein, e.g., Med1 or a transcription factor, or to an eRNA.

In embodiments the reaction mixture comprises:

a tissue component from a disease-state, e.g., cancerous, cell, e.g., chromosomal DNA, and one or both of:

a probe that binds selectively to a super-enhancer component, e.g. binds selectively to a protein, e.g., Med1 or a transcription factor, or to an eRNA; and a reagent capable of cross-linking, e.g., covalently cross-linking, nucleic acid, e.g., chromosomal or mitochondrial DNA, to a super-enhancer component.

In embodiments the reaction mixture comprises:

a tissue component from a disease-state, e.g., cancerous, cell, e.g., chromosomal DNA, cross-linked to a super-enhancer component, e.g. a protein, e.g., Med1 or a transcription factor, or to an eRNA; and

optionally, a probe that binds selectively to a super-enhancer component, e.g. binds selectively to a protein, e.g., Med1 or a transcription factor, or to an eRNA.

As used herein, the term “cancer” refers to a malignant neoplasm (Stedman's Medical Dictionary, 25th ed.; Hensyl ed.; Williams & Wilkins: Philadelphia, 1990). Exemplary cancers include, but are not limited to, acoustic neuroma; adenocarcinoma; adrenal gland cancer; anal cancer; angiosarcoma (e.g., lymphangiosarcoma, lymphangioendotheliosarcoma, hemangiosarcoma); appendix cancer; benign monoclonal gammopathy; biliary cancer (e.g., cholangiocarcinoma); bladder cancer; breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast); brain cancer (e.g., meningioma, glioblastomas, glioma (e.g., astrocytoma, oligodendroglioma), medulloblastoma); bronchus cancer; carcinoid tumor; cervical cancer (e.g., cervical adenocarcinoma); choriocarcinoma; chordoma; craniopharyngioma; colorectal cancer (e.g., colon cancer, rectal cancer, colorectal adenocarcinoma); connective tissue cancer; epithelial carcinoma; ependymoma; endotheliosarcoma (e.g., Kaposi's sarcoma, multiple idiopathic hemorrhagic sarcoma); endometrial cancer (e.g., uterine cancer, uterine sarcoma); esophageal cancer (e.g., adenocarcinoma of the esophagus, Barrett's adenocarinoma); Ewing's sarcoma; eye cancer (e.g., intraocular melanoma, retinoblastoma); familiar hypereosinophilia; gall bladder cancer; gastric cancer (e.g., stomach adenocarcinoma); gastrointestinal stromal tumor (GIST); germ cell cancer; head and neck cancer (e.g., head and neck squamous cell carcinoma, oral cancer (e.g., oral squamous cell carcinoma), throat cancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngeal cancer, oropharyngeal cancer)); hematopoietic cancers (e.g., leukemia such as acute lymphocytic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL), acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chronic lymphocytic leukemia (CLL) (e.g., B-cell CLL, T-cell CLL)); lymphoma such as Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) and non-Hodgkin lymphoma (NHL) (e.g., B-cell NHL such as diffuse large cell lymphoma (DLCL) (e.g., diffuse large B-cell lymphoma), follicular lymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), marginal zone B-cell lymphomas (e.g., mucosa-associated lymphoid tissue (MALT) lymphomas, nodal marginal zone B-cell lymphoma, splenic marginal zone B-cell lymphoma), primary mediastinal B-cell lymphoma, Burkitt lymphoma, lymphoplasmacytic lymphoma (i.e., Waldenström's macroglobulinemia), hairy cell leukemia (HCL), immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma and primary central nervous system (CNS) lymphoma; and T-cell NHL such as precursor T-lymphoblastic lymphoma/leukemia, peripheral T-cell lymphoma (PTCL) (e.g., cutaneous T-cell lymphoma (CTCL) (e.g., mycosis fungiodes, Sezary syndrome), angioimmunoblastic T-cell lymphoma, extranodal natural killer T-cell lymphoma, enteropathy type T-cell lymphoma, subcutaneous panniculitis-like T-cell lymphoma, and anaplastic large cell lymphoma); a mixture of one or more leukemia/lymphoma as described above; and multiple myeloma (MM)), heavy chain disease (e.g., alpha chain disease, gamma chain disease, mu chain disease); hemangioblastoma; hypopharynx cancer; inflammatory myofibroblastic tumors; immunocytic amyloidosis; kidney cancer (e.g., nephroblastoma a.k.a. Wilms' tumor, renal cell carcinoma); liver cancer (e.g., hepatocellular cancer (HCC), malignant hepatoma); lung cancer (e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung); leiomyosarcoma (LMS); mastocytosis (e.g., systemic mastocytosis); muscle cancer; myelodysplastic syndrome (MDS); mesothelioma; myeloproliferative disorder (MPD) (e.g., polycythemia vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a. myelofibrosis (MF), chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)); neuroblastoma; neurofibroma (e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis); neuroendocrine cancer (e.g., gastroenteropancreatic neuroendoctrine tumor (GEP-NET), carcinoid tumor); osteosarcoma (e.g., bone cancer); ovarian cancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma); papillary adenocarcinoma; pancreatic cancer (e.g., pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors); penile cancer (e.g., Paget's disease of the penis and scrotum); pinealoma; primitive neuroectodermal tumor (PNT); plasma cell neoplasia; paraneoplastic syndromes; intraepithelial neoplasms; prostate cancer (e.g., prostate adenocarcinoma); rectal cancer; rhabdomyosarcoma; salivary gland cancer; skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA), melanoma, basal cell carcinoma (BCC)); small bowel cancer (e.g., appendix cancer); soft tissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma); sebaceous gland carcinoma; small intestine cancer; sweat gland carcinoma; synovioma; testicular cancer (e.g., seminoma, testicular embryonal carcinoma); thyroid cancer (e.g., papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC), medullary thyroid cancer); urethral cancer; vaginal cancer; and vulvar cancer (e.g., Paget's disease of the vulva).

In embodiments the reaction mixture further comprises a probe selective for a preselected genetic signature, e.g., an SNP, e.g., a preselected genetic signature in a super-enhancer or in a gene under the control of a super enhancer.

In another aspect, the invention features a set of reaction mixtures, e.g., a set comprising at least two of the reaction mixtures described herein. In an embodiment the set comprises:

a reaction mixture comprising a probe selective for a preselected genetic signature, e.g., an SNP, e.g., a preselected genetic signature in a super-enhancer or in a gene under the control of a super enhancer; and

a reaction mixture comprises a probe which can be used to determine if a super-enhancer is present. E.g., the reaction mixture comprises one or both of: a probe that binds selectively to a super-enhancer component, e.g. binds selectively to a protein, e.g., Med1 or a transcription factor, or to an eRNA; and a reagent capable of cross-linking, e.g., covalently cross-linking, nucleic acid, e.g., chromosomal or mitochondrial DNA, to a super-enhancer component. Exemplary super-enhancer components include a protein, e.g., Med1 or a transcription factor, or to an eRNA.

In certain aspects, the present invention relates to a method of modifying a cell state or identity, comprising introducing into the cell a super-enhancer that is required to stabilize the cell state or identity. It is to be understood that the super-enhancers of the present invention are capable of modifying the cell state or identity of any cell in which it has been shown that the super-enhancer is required to stabilize the cell state or identity. In some embodiments, the cell state is an embryonic-stem cell like state. Upon introduction of the super-enhancer into the cell, the super-enhancer drives expression of genes that are required to maintain the cell state or identity associated with the super-enhancer.

In some aspects, cell state reflects the fact that cells of a particular type can exhibit variability with regard to one or more features and/or can exist in a variety of different conditions, while retaining the features of their particular cell type and not gaining features that would cause them to be classified as a different cell type. The different states or conditions in which a cell can exist may be characteristic of a particular cell type (e.g., they may involve properties or characteristics exhibited only by that cell type and/or involve functions performed only or primarily by that cell type) or may occur in multiple different cell types. Sometimes a cell state reflects the capability of a cell to respond to a particular stimulus or environmental condition (e.g., whether or not the cell will respond, or the type of response that will be elicited) or is a condition of the cell brought about by a stimulus or environmental condition. Cells in different cell states may be distinguished from one another in a variety of ways. For example, they may express, produce, or secrete one or more different genes, proteins, or other molecules (“markers”), exhibit differences in protein modifications such as phosphorylation, acetylation, etc., or may exhibit differences in appearance. Thus a cell state may be a condition of the cell in which the cell expresses, produces, or secretes one or more markers, exhibits particular protein modification(s), has a particular appearance, and/or will or will not exhibit one or more biological response(s) to a stimulus or environmental condition. Markers can be assessed using methods well known in the art, e.g., gene expression can be assessed at the mRNA level using Northern blots, cDNA or oligonucleotide microarrays, or sequencing (e.g., RNA-Seq), or at the level of protein expression using protein microarrays, Western blots, flow cytometry, immunohistochemistry, etc. Modifications can be assessed, e.g., using antibodies that are specific for a particular modified form of a protein, e.g., phospho-specific antibodies, or mass spectrometry.

Another example of cell state is “activated” state as compared with “resting” or “non-activated” state. Many cell types in the body have the capacity to respond to a stimulus by modifying their state to an activated state. The particular alterations in state may differ depending on the cell type and/or the particular stimulus. A stimulus could be any biological, chemical, or physical agent to which a cell may be exposed. A stimulus could originate outside an organism (e.g., a pathogen such as virus, bacteria, or fungi (or a component or product thereof such as a protein, carbohydrate, or nucleic acid, cell wall constituent such as bacterial lipopolysaccharide, etc) or may be internally generated (e.g., a cytokine, chemokine, growth factor, or hormone produced by other cells in the body or by the cell itself). For example, stimuli can include interleukins, interferons, or TNF alpha. Immune system cells, for example, can become activated upon encountering foreign (or in some instances host cell) molecules. Cells of the adaptive immune system can become activated upon encountering a cognate antigen (e.g., containing an epitope specifically recognized by the cell's T cell or B cell receptor) and, optionally, appropriate co-stimulating signals. Activation can result in changes in gene expression, production and/or secretion of molecules (e.g., cytokines, inflammatory mediators), and a variety of other changes that, for example, aid in defense against pathogens but can, e.g., if excessive, prolonged, or directed against host cells or host cell molecules, contribute to diseases. Fibroblasts are another cell type that can become activated in response to a variety of stimuli (e.g., injury (e.g., trauma, surgery), exposure to certain compounds including a variety of pharmacological agents, radiation, etc.) leading them, for example, to secrete extracellular matrix components. In the case of response to injury, such ECM components can contribute to wound healing. However, fibroblast activation, e.g., if prolonged, inappropriate, or excessive, can lead to a range of fibrotic conditions affecting diverse tissues and organs (e.g., heart, kidney, liver, intestine, blood vessels, skin) and/or contribute to cancer. The presence of abnormally large amounts of ECM components can result in decreased tissue and organ function, e.g., by increasing stiffness and/or disrupting normal structure and connectivity.

Another example of cell state reflects the condition of cell (e.g., a muscle cell or adipose cell) as either sensitive or resistant to insulin. Insulin resistant cells exhibit decreased response to circulating insulin; for example insulin-resistant skeletal muscle cells exhibit markedly reduced insulin-stimulated glucose uptake and a variety of other metabolic abnormalities that distinguish these cells from cells with normal insulin sensitivity.

As used herein, a “cell state associated gene” is a gene the expression of which is associated with or characteristic of a cell state of interest (and is often not associated with or is significantly lower in many or most other cell states) and may at least in part be responsible for establishing and/or maintaining the cell state. For example, expression of the gene may be necessary or sufficient to cause the cell to enter or remain in a particular cell state.

In some aspects, modulating a super-enhancer function shifts a cell from an “abnormal” state towards a more “normal” state. In some embodiments, modulating a super-enhancer function shifts a cell from a “disease-associated” state towards a state that is not associated with disease. A “disease-associated state” is a state that is typically found in subjects suffering from a disease (and usually not found in subjects not suffering from the disease) and/or a state in which the cell is abnormal, unhealthy, or contributing to a disease.

In some embodiments, the methods and compounds herein are of use to reprogram a somatic cell, e.g., to a pluripotent state. In some embodiments the methods and compounds are of use to reprogram a somatic cell of a first cell type into a different cell type. In some embodiments, the methods and compounds herein are of use to differentiate a pluripotent cell to a desired cell type.

In an embodiment, the method of modifying a cell state or identity can be used to reprogram a cell to a less differentiated state, such method comprising the steps of: (a) contacting a differentiated cell or population of cells with at least one reprogramming agent capable of reprogramming said cell to less differentiated state; (b) maintaining said cell or population of cells under conditions appropriate for proliferation of said cell population and for activity of said at least one reprogramming agent for a period of time sufficient to begin reprogramming of said cell or population of cells; and (c) transfecting said cell or population of cells with a nucleic acid construct comprising a super-enhancer having a plurality of binding sites for cognate transcription factors Oct4, Sox2, and Nanog, wherein transfection of said cell drives high levels of expression of embryonic stem cell genes required to reprogram and maintain the cell in a less differentiated state. In an embodiment, the less differentiated state is an embryonic stem cell-like state. Reprogramming of cells and suitable reprogramming agents (e.g., Oct4, Sox2, Nanog, etc.) are described in further detail in U.S. Patent Application Publication No. 2011/0076678, U.S. Pat. No. 7,682,828, U.S. Pat. No. 8,071,369, U.S. Patent Application Publication No. 2012/0028821, U.S. Patent Application Ser. No. 61/098,327, the teachings of all of which are incorporated herein by reference in their entirety.

In certain aspects, the present invention relates to a kit for reprogramming a differentiated somatic cell population to an embryonic stem-cell like state, comprising: (a) a population of differentiated somatic cells; (b) at least one reprogramming agent capable of reprogramming said cell to an embryonic stem cell-like state; and (c) a nucleic acid construct comprising a super-enhancer containing clusters of enhancers having binding sites for cognate transcription factors Oct4, Sox2, and Nanog; and (d) a reagent for transfecting said population of cells with said nucleic acid construct.

In some embodiments, modulating a function (activity) of a super-enhancer is of use to treat, e.g., a metabolic, neurodegenerative, inflammatory, auto-immune, proliferative, infectious, cardiovascular, musculoskeletal, or other disease. It will be understood that diseases can involve multiple pathologic processes and mechanisms and/or affect multiple body systems. Discussion herein of a particular disease in the context of a particular pathologic process, mechanism, cell state, cell type, or affected organ, tissue, or system, should not be considered limiting. For example, a number of different tumors (e.g., hematologic neoplasms such as leukemias) arise from undifferentiated progenitor cells and/or are composed largely of undifferentiated or poorly differentiated cells that retain few if any distinctive features characteristic of differentiated cell types. These tumors, which are sometimes termed undifferentiated or anaplastic tumors, may be particularly aggressive and/or difficult to treat. In some embodiments of the invention, a method of the invention is used to modify such cells to a more differentiated state, which may be less highly proliferative and/or more amenable to a variety of therapies, e.g., chemotherapeutic agents. In another embodiment, an inventive method is used to treat insulin resistance which occurs, for example, in individuals suffering from type II diabetes and pre-diabetic individuals. It would be beneficial to modify the state of insulin-resistant cells towards a more insulin-sensitive state, e.g., for purposes of treating individuals who are developing or have developed insulin resistance. In another embodiment, an inventive method is used to treat obesity.

Many inflammatory and/or autoimmune conditions may occur at least in part as a result of excessive and/or inappropriate activation of immune system cells. Autoimmune diseases include, e.g., Graves disease, Hashimoto's thyroiditis, myasthenia gravis, rheumatoid arthritis, sarcoidosis, Sjögren's syndrome, scleroderma, ankylosing spondylitis, type I diabetes, vasculitis, and lupus erythematosus. Furthermore, immune-mediated rejection is a significant risk in organ and tissue transplantation. Inflammation plays a role in a large number of diseases and conditions. Inflammation can be acute (and may be recurrent) or chronic. In general, inflammation can affect almost any organ, tissue, or body system. For example, inflammation can affect the cardiovascular system (e.g., heart), musculoskeletal system, respiratory system (e.g., bronchi, lungs), renal system, (e.g., kidneys), eyes, nervous system, gastrointestinal system (e.g., colon), integumentary system (e.g., skin), musculoskeletal system (e.g., joints, muscles), resulting in a wide variety of conditions and diseases. Chronic inflammation is increasingly recognized as an important factor contributing to atherosclerosis and degenerative diseases of many types. Inflammation influences the microenvironment around tumours and contributes, e.g., to tumor cell proliferation, survival and migration. Furthermore, chronic inflammation can eventually lead to fibrosis.

Exemplary inflammatory diseases include, e.g., adult respiratory distress syndrome (ARDS), atherosclerosis (e.g., coronary artery disease, cerebrovascular disease), allergies, asthma, cancer, demyelinating diseases, dermatomyositis, inflammatory bowel disease (e.g., Crohn's disease, ulcerative colitis), inflammatory myopathies, multiple sclerosis, glomerulonephritis, psoriasis, pancreatitis, rheumatoid arthritis, sepsis, vasculitis (including phlebitis and arteritis, e.g., polyarteritis nodosa, Wegener's granulomatosis, Buerger's disease, Takayasu's arteritis, etc.). In some embodiments, a method of the invention is used to modify immune cell state to reduce activation of immune system cells involved in such conditions and/or render immune system cells tolerant to one or more antigens. In one embodiment, dendritic cell state is altered. Promoting immune system activation using a method of the invention (e.g., in individuals who have immunodeficiencies or have been treated with drugs that deplete or damage immune system cells), potentially for limited periods of time, may be of benefit in the treatment of infectious diseases.

In other embodiments, activated fibroblasts are modified to a less activated cell state to reduce or inhibit fibrotic conditions or treat cancer.

Post-surgical adhesions can be a complication of, e.g., abdominal, gynecologic, orthopedic, and cardiothoracic surgeries. Adhesions are associated with considerable morbidity and can be fatal. Development of adhesions involves inflammatory and fibrotic processes. In some embodiments, a method of the invention is used to modify state of immune system cells and/or fibroblasts to prevent or reduce adhesion formation or maintenance.

In an embodiment, a gene associated with one or a metabolic, neurodegenerative, inflammatory, auto-immune, proliferative, infectious, cardiovascular, musculoskeletal, or other disease is regulated by a super-enhancer, and the method comprises administering an agent that disrupts the super-enhancer. In some embodiments, the gene comprises a disease-associated DNA variant such as a SNP.

In other embodiments, modifying cells to a more or less differentiated state is of use to generate a population of cells in vivo that aid in repair or regeneration of a diseased or damaged organ or tissue, or to generate a population of cells ex vivo that is then administered to a subject to aid in repair or regeneration of a diseased or damaged organ or tissue.

In some embodiments, cell type and/or cell state becomes modified over the course of multiple cell cycle(s). In some embodiments, cell type and/or cell state is stably modified. In some embodiments, a modified type or state may persist for varying periods of time (e.g., days, weeks, months, or indefinitely) after the cell is no longer exposed to the agent(s) that caused the modification. In some embodiments, continued or at intermittent exposure to the agent(s) is required or helpful to maintain the modified state or type.

Cells may be in living animal, e.g., a mammal, or may be isolated cells. Isolated cells may be primary cells, such as those recently isolated from an animal (e.g., cells that have undergone none or only a few population doublings and/or passages following isolation), or may be a cell of a cell line that is capable of prolonged proliferation in culture (e.g., for longer than 3 months) or indefinite proliferation in culture (immortalized cells). In many embodiments, a cell is a somatic cell. Somatic cells may be obtained from an individual, e.g., a human, and cultured according to standard cell culture protocols known to those of ordinary skill in the art. Cells may be obtained from surgical specimens, tissue or cell biopsies, etc. Cells may be obtained from any organ or tissue of interest. In some embodiments, cells are obtained from skin, lung, cartilage, breast, blood, blood vessel (e.g., artery or vein), fat, pancreas, liver, muscle, gastrointestinal tract, heart, bladder, kidney, urethra, prostate gland.

In some embodiments the cell is a mammalian cell. In some embodiments the cell is a human cell. In some embodiments the cell is an embryonic stem cell or embryonic stem cell-like cell. In some embodiments the cell is a muscle cell. In some embodiments the muscle cell is a myotube. In some embodiments the cell is a B cell. In some embodiments the B cell is a Pro-B cell.

In some embodiments the cell is from the brain. In some embodiments the cell is an astrocyte cell. In some embodiments the cell is from the angular gyms of the brain. In some embodiments the cell is from the anterior caudate of the brain. In some embodiments the cell is from the cingulate gyms of the brain. In some embodiments the cell is from the hippocampus of the brain. In some embodiments the cell is from the inferior temporal lobe of the brain. In some embodiments the cell is from the middle frontal lobe of the brain.

In some embodiments the cell is a naïve T cell. In some embodiments the cell is a memory T cell. In some embodiments the cell is CD4 positive. In some embodiments the cell is CD25 positive. In some embodiments the cell is CD45RA positive. In some embodiments the cell is CD45RO positive. In some embodiments the cell is IL-17 positive. In some embodiments the cell is stimulated with PMA. In some embodiments the cell is a Th cell. In some embodiments the cell is a Th17 cell. In some embodiments the cell is CD255 positive. In some embodiments the cell is CD127 positive. In some embodiments the cell is CD8 positive. In some embodiments the cell is CD34 positive.

In some embodiments the cell is from the duodenum. In some embodiments the cell is from smooth muscle tissue of the duodenum.

In some embodiments the cell is from skeletal muscle tissue. In some embodiments the cell is a myoblast cell. In some embodiments the cell is a myotube cell.

In some embodiments the cell is from the stomach. In some embodiments the cell is from smooth muscle tissue of the stomach.

In some embodiments the cell is CD3 positive. In some embodiments the cell is CD8 positive. In some embodiments the cell is CD14 positive. In some embodiments the cell is CD19 positive. In some embodiments the cell is CD20 positive. In some embodiments the cell is CD34 positive. In some embodiments the cell is CD56 positive.

In some embodiments the cell is from the colon. In some embodiments the cell is a crypt cell. In some embodiments the cell is a colon crypt cell.

In some embodiments the cell is from the intestine. In some embodiments the cell is from the large intestine. In some embodiments the intestine is from a fetus.

In some embodiments the cell is a DND41 cell. In some embodiments the cell is a GM12878 cell. In some embodiments the cell is a H1 cell. In some embodiments the cell is a H2171 cell. In some embodiments the cell is a HCC1954 cell. In some embodiments the cell is a HCT-116 cell. In some embodiments the cell is a HeLa cell. In some embodiments the cell is a HepG2 cell. In some embodiments the cell is a HMEC cell. In some embodiments the cell is a HSMM tube cell. In some embodiments the cell is a HUVEC cell. In some embodiments the cell is a IMR90 cell. In some embodiments the cell is a Jurkat cell. In some embodiments the cell is a K562 cell. In some embodiments the cell is a LNCaP cell. In some embodiments the cell is a MCF-7 cell. In some embodiments the cell is a MM1 S cell. In some embodiments the cell is a NHLF cell. In some embodiments the cell is a NHDF-Ad cell. In some embodiments the cell is a RPMI-8402 cell. In some embodiments the cell is a U87 cell.

In some embodiments the cell is an osteoblast cell. In some embodiments the cell is from the pancreas. In some embodiments the cell is from a pancreatic cancer cell.

In some embodiments the cell is from adipose tissue. In some embodiments the cell is from the adrenal gland. In some embodiments the cell is from the bladder. In some embodiments the cell is from the esophagus. In some embodiments the cell is from the stomach. In some embodiments the cell is a gastric cell. In some embodiments the cell is from the left ventricle. In some embodiments the cell is from the lung. In some embodiments the cell is from a lung cancer cell. In some embodiments the cell is a fibroblast cell.

In some embodiments the cell is from the ovary. In some embodiments the cell is from the psoas muscle. In some embodiments the cell is from the right atrium. In some embodiments the cell is from the right ventricle. In some embodiments the cell is from the sigmoid colon. In some embodiments the cell is from the small intestine. In some embodiments the cell is from the spleen. In some embodiments the cell is from the thymus.

In some embodiments the cell is a VACO 9M cell. In some embodiments the cell is a VACO 400 cell. In some embodiments the cell is a VACO 503 cell. In some embodiments the cell is from the aorta.

In some embodiments the cell is from the brain. In some embodiments the cell is a brain cancer cell.

In some embodiments the cell is from the breast. In some embodiments the cell is a breast cancer cell.

In some embodiments the cell is from the cervix. In some embodiments the cell is a cervical cancer cell.

In some embodiments the cell is from the colon. In some embodiments the cell is from a colorectal cancer cell.

In some embodiments the cell is a blood cell. In some embodiments the blood cell is a monocyte cell. In some embodiments the blood cell is a B cell. In some embodiments the blood cell is a T cell. In some embodiments the blood cell is a human embryonic stem cell. In some embodiments the blood cell is a cancerous blood cell. In some embodiments the blood cell is from a fetus.

In some embodiments the cell is from bone. In some embodiments the bone cell is an osteoblast cell.

In some embodiments the cell is from the heart. In some embodiments the cell is a mammary epithelial cell. In some embodiments the cell is a skin cell. In some embodiments the skin cell is a fibroblast cell.

In some embodiments the cell is an embryonic stem cell. In some embodiments the cell is from the umbilical vein. In some embodiments the cell from the umbilical vein is an endothelial cell.

In some embodiments the cell is from the colon. In some embodiments the cell is from the prostate. In some embodiments the cell is a prostate cancer cell.

In some embodiments the cell is from the liver. In some embodiments the cell is a liver cancer cell.

In some embodiments the cell is from the muscle. In some embodiments the muscle is from a fetus.

In some embodiments the cell is from the thymus. In some embodiments the thymus is from a fetus.

Cells may be maintained in cell culture following their isolation. In certain embodiments, the cells are passaged or allowed to double once or more following their isolation from the individual (e.g., between 2-5, 5-10, 10-20, 20-50, 50-100 times, or more) prior to their use in a method of the invention. They may be frozen and subsequently thawed prior to use. In some embodiments, the cells will have been passaged or permitted to double no more than 1, 2, 5, 10, 20, or 50 times following their isolation from the individual prior to their use in a method of the invention. Cells may be genetically modified or not genetically modified in various embodiments of the invention. Cells may be obtained from normal or diseased tissue. In some embodiments, cells are obtained from a donor, and their state or type is modified ex vivo using a method of the invention. The modified cells are administered to a recipient, e.g., for cell therapy purposes. In some embodiments, the cells are obtained from the individual to whom they are subsequently administered.

A population of isolated cells in any embodiment of the invention may be composed mainly or essentially entirely of a particular cell type or of cells in a particular state. In some embodiments, an isolated population of cells consists of at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% cells of a particular type or state (i.e., the population is at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% pure), e.g., as determined by expression of one or more markers or any other suitable method.

In certain aspects, the present invention relates to a method of selectively inhibiting expression of an aberrantly expressed gene comprising disrupting the function of a super-enhancer associated with the gene. In certain embodiments, the gene comprises an oncogene. During the course of work described herein, the present inventors have observed that disruption of super-enhancers by BRD4 inhibition led to a dramatic loss of expression of critical tumor genes, accompanied by a potent antiproliferative effect. Given the fact that super-enhancers are common features of mammalian cells, and that super-enhancers have been shown to drive high levels of gene expression, it is reasonable to expect that super-enhancer disruption can be used to selectively inhibit expression of any gene (e.g., any gene that is overexpressed in a diseased cell, wherein the gene is associated with a super-enhancer) by disrupting the super-enhancer associated with the oncogene. In an embodiment, the oncogene is MYC. In an embodiment, the oncogene is IRF4.

In certain aspects, the present invention relates to a method of selectively inhibiting expression of a gene associated with a hallmark of a disease (e.g., cancer), the method comprising disrupting the function of a super-enhancer associated with the gene. In some embodiments, the gene comprises a disease-associated DNA sequence variation such as a SNP.

It should be appreciated that the present invention contemplates the use of any technique or any agent that is capable of disrupting the function of the super-enhancer. Generally, disrupting the function of the super-enhancer involves contacting said super-enhancer region with an effective amount of an agent that interferes with occupancy of the super-enhancer region by a cognate transcription factor for the gene, a transcriptional coactivator, or a chromatin regulator. In some embodiments, disrupting the function of the super-enhancer can be achieved by contacting the super-enhancer region with a pause release agent. In certain embodiments, the agent interferes with a binding site on the super-enhancer for the cognate transcription factor, interferes with interaction between the cognate transcription factor and a transcriptional coactivator, inhibits the transcription coactivator, or interferes with or inhibits the chromatin regulator. In some embodiments, the agent is a bromodomain inhibitor. In some embodiments, the agent is a BRD4 inhibitor. In some embodiments, the agent is the compound JQ1. In some embodiments, the agent is iBET.

Any of a wide variety of agents (also termed “compounds”) can be used to disrupt the function of the super-enhancer, such as BET bromodomain inhibitors, P-TEFb inhibitors or compounds that interfere with binding of the cognate transcription factors to the binding sites of the super-enhancer associated with the gene (e.g, if the gene is an oncogene, such as MYC, a c-Myc inhibitor can be used to disrupt the function of the super-enhancer). An inhibitor could be any compound that, when contacted with a cell, results in decreased functional activity of a molecule or complex, e.g., transcriptional coactivator (e.g., Mediator), a chromatin regulator (e.g., BRD4), an elongation factor (e.g., P-TEFb), or cognate transcription factor (e.g., a cognate oncogenic transcription factor), in the cell. An inhibitor could act directly, e.g., by physically interacting with a molecule or complex to be inhibited, or a component thereof, or indirectly such as by interacting with a different molecule or complex required for activity of the molecule or complex to be inhibited, or by interfering with expression or localization.

Compounds of use in various embodiments of the invention can comprise, e.g., small molecules, peptides, polypeptides, nucleic acids, oligonucleotides, etc. Certain non-limiting examples are presented below.

A small molecule is often an organic compound having a molecular weight equal to or less than 2.0 kD, e.g., equal to or less than 1.5 kD, e.g., equal to or less than 1 kD, e.g., equal to or less than 500 daltons and usually multiple carbon-carbon bonds. Small molecules often comprise one or more functional groups that mediate structural interactions with proteins, e.g., hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, and in some embodiments at least two of the functional chemical groups. A small molecule may comprise cyclic carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more chemical functional groups and/or heteroatoms. In some embodiments a small molecule satisfies at least 3, 4, or all criteria of Lipinski's “Rule of Five”. In some embodiments, a compound is cell-permeable, e.g., within the range of typical compounds that act intracellularly, e.g., within mammalian cells. In some embodiments, the IC50 of a compound, e.g., a small molecule, for a target to be inhibited is less than or equal to about 5 nM, 10 nM, 50 nM, 100 nM, 500 nM, 1 μM, 10 μM, 50 μM, or 100 μM,

Nucleic acids, e.g., oligonucleotides (which typically refers to short nucleic acids, e.g., 50 nucleotides in length or less), the invention contemplates use of oligonucleotides that are single-stranded, double-stranded (ds), blunt-ended, or double-stranded with overhangs, in various embodiments of the invention. The full spectrum of modifications (e.g., nucleoside and/or backbone modifications), non-standard nucleotides, delivery vehicles and systems, etc., known in the art as being useful in the context of siRNA or antisense-based molecules for research or therapeutic purposes is contemplated for use in various embodiments of the instant invention. In some embodiments a compound is an RNAi agent, antisense oligonucleotide, or aptamer. The term “RNAi agent” encompasses nucleic acids that can be used to achieve RNA silencing in mammalian cells. As used herein RNA silencing, also termed RNA interference (RNAi), encompasses processes in which sequence-specific silencing of gene expression is effected by an RNA-induced silencing complex (RISC) that has a short RNA strand incorporated therein, which strand directs or “guides” sequence-specific degradation or translational repression of mRNA to which it has complementarity. The complementarity between the short RNA and mRNA need not be perfect (100%) but need only be sufficient to result in inhibition of gene expression. For example, the degree of complementarity and/or the characteristics of the structure formed by hybridization of the mRNA and the short RNA strand can be such that the strand can (i) guide cleavage of the mRNA in the RNA-induced silencing complex (RISC) and/or (ii) cause translational repression of the mRNA by RISC. The short RNA is often incorporated into RISC as part of a short double-stranded RNA (dsRNA). RNAi may be achieved artificially in eukaryotic, e.g., mammalian, cells in a variety of ways. For example, RNAi may be achieved by introducing an appropriate short double-stranded nucleic acid into the cells or expressing in the cells a nucleic acid that is processed intracellularly to yield such short dsRNA. Exemplary RNAi agents are a short hairpin RNA (shRNA), a short interfering RNA (siRNA), micrRNA (miRNA) and a miRNA precursor. siRNAs typically comprise two separate nucleic acid strands that are hybridized to each other to form a duplex. They can be synthesized in vitro, e.g., using standard nucleic acid synthesis techniques. A nucleic acid may contain one or more non-standard nucleotides, modified nucleosides (e.g., having modified bases and/or sugars) or nucleotide analogs, and/or have a modified backbone. Any modification or analog recognized in the art as being useful for RNAi, aptamers, antisense molecules or other uses of oligonucleotides can be used. Some modifications result in increased stability, cell uptake, potency, etc. Exemplary compound can comprise morpholinos or locked nucleic acids. In some embodiments the nucleic acid differs from standard RNA or DNA by having partial or complete 2′-O-methylation or 2′-O-methoxyethyl modification of sugar, phosphorothioate backbone, and/or a cholesterol-moiety at the 3′-end. In certain embodiments the siRNA or shRNA comprises a duplex about 19 nucleotides in length, wherein one or both strands has a 3′ overhang of 1-5 nucleotides in length (e.g., 2 nucleotides), which may be composed of deoxyribonucleotides. shRNA comprise a single nucleic acid strand that contains two complementary portions separated by a predominantly non-self-complementary region. The complementary portions hybridize to form a duplex structure and the non-self-complementary region forms a loop connecting the 3′ end of one strand of the duplex and the 5′ end of the other strand. shRNAs can undergo intracellular processing to generate siRNAs. In certain embodiments the term “RNAi agent” also encompasses vectors, e.g., expression vectors, that comprise templates for transcription of an siRNA (e.g., as two separate strands that can hybridize), shRNA, or microRNA precursor, and can be used to introduce such template into mammalian cells and result in transient or stable expression thereof.

In some embodiments an RNAi agent, aptamer, antisense oligonucleotide, other nucleic acid, peptide, polypeptide, or small molecule is physically associated with a moiety that increases cell uptake, such as a cell-penetrating peptide, or a delivery agent. In some embodiments a delivery agent at least in part protects the compound from degradation, metabolism, or elimination from the body (e.g., increases the half-life). A variety of compositions and methods can be used to deliver agents to cells in vitro or in vivo. For example, compounds can be attached to a polyalkylene oxide, e.g., polyethylene glycol (PEG) or a derivative thereof, or incorporated into or attached to various types of molecules or particles such as liposomes, lipoplexes, or polymer-based particles, e.g., microparticles or nanoparticles composed at least in part of one or more biocompatible polymers or copolymers comprising poly(lactide-glycolide), copolyoxalates, polycaprolactones, polyesterar des, polyorthoesters, polyhydroxybutyric acid, and/or polyanhydrides.

In some embodiments, an agent comprises a polypeptide. A “polypeptide” refers to a polymer of amino acids linked by peptide bonds. A protein is a molecule comprising one or more polypeptides. A peptide is a relatively short polypeptide, typically between about 2 and 100 amino acids (aa) in length, e.g., between 4 and 60 aa; between 8 and 40 aa; between 10 and 30 aa. The terms “protein”, “polypeptide”, and “peptide” may be used interchangeably. In general, a polypeptide may contain only standard amino acids or may comprise one or more non-standard amino acids (which may be naturally occurring or non-naturally occurring amino acids) and/or amino acid analogs in various embodiments. A “standard amino acid” is any of the 20 L-amino acids that are commonly utilized in the synthesis of proteins by mammals and are encoded by the genetic code. A “non-standard amino acid” is an amino acid that is not commonly utilized in the synthesis of proteins by mammals. Non-standard amino acids include naturally occurring amino acids (other than the 20 standard amino acids) and non-naturally occurring amino acids. In some embodiments, a non-standard, naturally occurring amino acid is found in mammals. For example, ornithine, citrulline, and homocysteine are naturally occurring non-standard amino acids that have important roles in mammalian metabolism. Exemplary non-standard amino acids include, e.g., singly or multiply halogenated (e.g., fluorinated) amino acids, D-amino acids, homo-amino acids, N-alkyl amino acids (other than proline), dehydroamino acids, aromatic amino acids (other than histidine, phenylalanine, tyrosine and tryptophan), and α,α disubstituted amino acids. An amino acid, e.g., one or more of the amino acids in a polypeptide, may be modified, for example, by addition, e.g., covalent linkage, of a moiety such as an alkyl group, an alkanoyl group, a carbohydrate group, a phosphate group, a lipid, a polysaccharide, a halogen, a linker for conjugation, a protecting group, etc. Modifications may occur anywhere in a polypeptide, e.g., the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. A given polypeptide may contain many types of modifications. Polypeptides may be branched or they may be cyclic, with or without branching. Polypeptides may be conjugated with, encapsulated by, or embedded within a polymer or polymeric matrix, dendrimer, nanoparticle, microparticle, liposome, or the like. Modification may occur prior to or after an amino acid is incorporated into a polypeptide in various embodiments. Polypeptides may, for example, be purified from natural sources, produced in vitro or in vivo in suitable expression systems using recombinant DNA technology (e.g., by recombinant host cells or in transgenic animals or plants), synthesized through chemical means such as conventional solid phase peptide synthesis, and/or methods involving chemical ligation of synthesized peptides (see, e.g., Kent, S., J Pept Sci., 9(9):574-93, 2003 or U.S. Pub. No. 20040115774), or any combination of the foregoing.

One of ordinary skill in the art will understand that a protein may be composed of a single amino acid chain or multiple chains associated covalently or noncovalently. In some embodiments, the agent is a non-functional mutant of the cognate oncogenic transcription factor, the transcriptional coactivator, or the chromatin regulator that mimics interactions of the cognate oncogenic transcription factor, the transcriptional coactivator, or the chromatin regulator but lacks the ability to activate transcription of the oncogene. For example, a polypeptide can be a dominant negative version of Mediator, an elongation factor (e.g., P-TEFb subunit) or a dominant negative version of a cognate oncogenic transcription factor (e.g., a c-Myc or Max). A polypeptide that binds to and inhibits Mediator or P-TEFb or c-Myc could be identified, e.g., using phage display.

In some embodiments a compound comprises an antibody. The term “antibody” encompasses immunoglobulins and derivatives thereof containing an immunoglobulin domain capable of binding to an antigen. An antibody can originate from any mammalian or avian species, e.g., human, rodent (e.g., mouse, rabbit), goat, chicken, etc., or can be generated using, e.g., phage display. The antibody may be a member of any immunoglobulin class, e.g., IgG, IgM, IgA, IgD, IgE, or subclasses thereof such as IgG1, IgG2, etc. In various embodiments of the invention “antibody” refers to an antibody fragment such as an Fab′, F(ab′)2, scFv (single-chain variable) or other fragment that retains an antigen binding site, or a recombinantly produced scFv fragment, including recombinantly produced fragments. An antibody can be monovalent, bivalent or multivalent in various embodiments. The antibody may be a chimeric or “humanized” antibody, which can be generated using methods known in the art. An antibody may be polyclonal or monoclonal, though monoclonal antibodies may be preferred. Methods for producing antibodies that specifically bind to virtually any molecule of interest are known in the art. In some aspects the antibody is an intrabody, which may be expressed intracellularly. In some embodiments a compound comprises a single-chain antibody and a protein transduction domain (e.g., as a fusion polypeptide).

In some embodiments, a composition or method of the invention employs a transcriptional coactivator inhibitor, a chromatin regulator inhibitor, an elongation factor or pause release inhibitor, or a cognate transcription factor inhibitor that are small molecules.

In some embodiments, the agent is a BET bromodomain inhibitor. In some embodiments, the agent is a BRD4 inhibitor. In some embodiments, the agent is JQ1. In some embodiments, the agent is iBET. In some embodiments, the elongation factor or pause release inhibitor is a P-TEFb inhibitor. In some embodiments, the cognate oncogenic transcription factor inhibitor is a c-Myc inhibitor. In some embodiments, a composition or method employs a Mediator inhibitor, a BRD4 inhibitor, a P-TEFb inhibitor and a c-Myc inhibitor that each comprise a nucleic acid, e.g., RNAi agents. In some embodiments, a composition or method employs a Mediator inhibitor, a P-TEFb inhibitor that comprises a nucleic acid, e.g., RNAi agents, e.g., siRNAs. In some embodiments, the Mediator inhibitor may bind to a Mediator component, Mediator complex, or a Mediator associated protein, for example, an antibody directed against the Mediator component, Mediator complex, or the Mediator associated protein. Examples of suitable antibodies can be found in PCT International Application No. WO 2011/100374, the teachings of which are incorporated herein by reference in their entirety.

In some embodiments the material is isolated using an agent (e.g., an antibody) that binds to a Mediator component, Mediator complex, or that binds to a Mediator-associated protein.

In some embodiments, the agent is a nucleic acid that hybridizes to a binding site on the super-enhancer for the cognate transcription factor.

Compounds can be produced using any suitable method known in the art. The skilled artisan will select an appropriate method based, e.g., on the nature of the compound. The production method can be partially or completely synthetic in various embodiments. In some embodiments a compound (or starting material for synthesis) is purified from an organism or other natural source, e.g., a plant, microbe, fermentation broth, etc. A compound of use in the invention may be provided as part of a composition, which may contain, e.g., an ion, salt, aqueous or non-aqueous diluent or carrier, buffer, preservative, etc. It is noted that although combined use of compounds is of particular interest, the use of compounds disclosed herein is not limited to their use in combination. In some embodiments of the invention, a compound may be used as a single agent.

In some embodiments, a P-TEFb inhibitor inhibits CDK9 kinase activity. The compound may inhibit one or more additional kinases, e.g., CDKs, in addition to CDK9. Often a kinase inhibitor acts by binding to an ATP binding pocket of a kinase. Thus in some embodiments a CDK9 inhibitor binds to the ATP binding pocket of CDK9. In some embodiments the P-TEFb inhibitor is selective for CDKs relative to many, most, or all other kinase families. In some embodiments the CDK inhibitor is selective for CDKs 1, 4, and 9 versus CDK2. In some embodiments the P-TEFb inhibitor is a CDK inhibitor that is selective for CDK9 versus CDK2. In some embodiments the P-TEFb inhibitor is a CDK inhibitor that is selective for CDK9 versus CDK1 and CDK4. It will be appreciated that kinase inhibitory activity is tested against CKDs in complex with a preferred cyclin partner. For example, in some embodiments CDK2 activity can be tested using cyclin A. It will also be appreciated that a kinase assay can employ a relevant substrate, e.g., a physiologically relevant substrate or portion thereof comprising a phosphorylation site for the kinase.

In some embodiments, the compound is an N-methylpiperidinyl, chlorophenyl flavone. In some embodiments, the compound is flavopiridol or a flavopiridol analog.

Flavopiridol (−)-2-(2-Chlorophenyl)-5,7-dihydroxy-8-[(3S,4R)-3-hydroxy-1-methyl-4-piperidinyl]-4H-1-benzopyran-4-one hydrochloride is a synthetic flavone that inhibits multiple CDKs, including CDK9. Its structure is shown below.

Flavopiridol has been shown to have antitumor activity against various tumor cells lines and to inhibit tumor growth in xenograft models. It has undergone clinical trials in a number of different cancer types including various solid tumors and leukemias. As described further in the examples, flavopiridol was shown to inhibit pause release. Without wishing to be bound by theory, this may help counteract the effects of Myc overexpression, and this may be the basis for the therapeutic effect of flavopiridol on some tumors.

Flavopiridol analogs include compounds designed based on flavopiridol, e.g., by modifying one or more of the rings of the flavopiridol structure at one or more positions. In some embodiments, a flavopiridol analog is a 2-thio or 2-oxo flavopiridol analog. For example, PCT/US 1997/007610 describes compounds of formula I:

wherein X is oxygen or sulfur; R¹, R², R³, R⁴, R⁵, R⁶, m, and n are as defined in PCT/US 1997/007610.

Additional flavopiridol analogs are disclosed in Murthi, K. K., et al., Bioorg Med Chem Lett. 10(10): 1037-41, 2000, which describes modifications of the 3-hydroxy-1-methylpiperidinyl (D ring) of flavopiridol.

In some embodiments, a flavopiridol analog has the following structure:

In some embodiments R is phenyl or substituted phenyl, e.g., halogenated phenyl. In some embodiments, R is selected from the group consisting of: 3-chlorophenyl, 4-chlorophenyl, 2-fluorophenyl, 4-fluorophenyl, 4-bromophenyl, 4-t-butylphenyl, 4-trifluoromethylphenyl, 4-hydroxyphenyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 4-chloro-3-pyridyl, 5-methylisoxazole, 3-vinylphenyl, 4-vinylphenyl, 2-chlorophenyl, 4-fluorophenyl, 2-bromophenyl, and 3-pyridyl. In some embodiments the compound displays increased selectivity for CDK9 than does flavopiridol. See, e.g., Ali, A., et al., Chembiochem, 10(12):2072-80, 2009, for additional information regarding these compound.

In some embodiments, a CDK9 inhibitor has the following structure:

wherein R1, R2, R3, R4, and R9 are as defined in PCT/IB 2006/052002 (WO/2007/148158). In some embodiments (i) R1 comprises an aromatic group; (ii) R4 comprises an R—(OH) group, wherein R is a C₁₋₆ aliphatic group; (iii) R9 comprises a C₁₋₆ aliphatic group, e.g, a methyl group; or (iv) any combination of (i), (ii), and (iii). In some embodiments, the compound may have the following structure:

wherein R comprises an aromatic group.

Crystal structures of P-TEFb (CDK9/cyclin T1) alone and in a complex with flavopiridol are available (Baumli, S., et al., EMBO J. 27(13): 1907-18, 2008). Flavopiridol was shown to bind to the ATP binding pocket of CDK9. Structural information can be used in the design of additional P-TEFb inhibitors including, but not limited to, additional analogs of flavopiridol. Furthermore, virtual screening can be performed using structural information regarding diverse chemical compounds to identify candidate P-TEFb inhibitors. In some embodiments, a P-TEFb inhibitor is a compound that makes similar intermolecular contacts with CDK9 as does flavopiridol. Similar approaches can be used to design analogs of other CDK9 inhibitors.

In some embodiments, a flavopiridol analog exhibiting reduced binding to human serum relative to flavopiridol is used.

In some embodiments, the P-TEFb inhibitor is a purine or purine analog, e.g., a biaryl purine analog. In some embodiments, the purine analog is a 2,6,9-substituted purine analog. In some embodiments, the compound is roscovitine, e.g., S-roscovitine or R-roscovitine. Unless otherwise indicated, where roscovitine is mentioned herein, the roscovitine can be R-roscovitine (also called Seliciclib or CYC202; 2-(R)-(1-Ethyl-2-hydroxyethylamino)-6-benzylamino-9-isopropyl purine). Roscovitine is a CDK inhibitor that preferentially inhibit multiple enzyme targets including CDK1, CDK2, CDK7 and CDK9 and has been studied in clinical trials for treatment of a variety of proliferative diseases.

In some embodiments the compound is a roscovatine analog. Exemplary roscovitine analogs are oloumicine (2-(2-hydroxyethylamino)-6-benzylamino-9-methylpurine), olomoucine II (6-[(2-hydroxybenzyl)amino]-2-[[1-(hydroxymethyl)propyl]amino]-9-isopropylpurine) and LGR1406 (N-5-(2-aminocyclohexyl)-N-7-benzyl-3-isopropyl-1(2)H-pyrazolo[4,3-d]pyrimidine-5,7-di-amine). Roscovitine analogs generated by introduction of an aryl ring onto the 4-position of the C-6 benzyl amino group of roscovitine, and a series of C-6 biarylmethylamino derivatives prepared with modifications on the C-6 biaryl rings, N-9 and C-2 positions, are described in Trova, M P, et. al., Bioorg Med Chem Lett. 19(23):6608-12, 2009.

Many additional CDK inhibitors are known in the art that may inhibit CDK9, optionally with at least some selectivity relative to inhibition of one or more other CDKs. For example, PCT/US2009/049637 (WO/2010/003133) discloses compounds that are reported to inhibit CDK9. In some aspects, the compounds have the following structure, where R1 and R3 are as defined therein.

PCT/EP2008/063715 (WO 2009047359) discloses additional compounds that are reported to inhibit CDK9. In some aspects, the compounds have the following structure, wherein R1, R2, Ra, and (R3)_(x) are as defined therein.

In some embodiments, a P-TEFb inhibitor comprises an RNAi agent (e.g., an siRNA) or an antisense oligonucleotide that inhibits expression of a P-TEFb subunit (e.g., CDK9, cyclin T1, T2a, T2b, or K). In some embodiments a P-TEFb inhibitor comprises an antibody or aptamer that specifically binds to a P-TEFb subunit. Optionally the antibody or aptamer may bind to multiple CDKs or cyclins.

In some embodiments, a c-Myc inhibitor is a small molecule. In some embodiments, a c-Myc inhibitor inhibits formation of c-Myc/Max heterodimers. In some embodiments, a c-Myc inhibitor inhibits binding of c-Myc/Max to a target site in DNA. In some embodiments a c-Myc inhibitor is relatively specific for inhibiting transcription mediated by c-Myc relative to transcription mediated by many or most other basic helix-loop-helix/leucine zipper transcription factors.

Various compounds that inhibit c-Myc are described in Berg, T., Curr. Op. Chem. Biol., 12: 464-471, 2008, and references therein. The peptide mimetic IIA6B17 is described in Berg, T., et al., Proc Natl Acad Sci USA 99 (2002), pp. 3830-3835 and was shown to inhibit c-Myc-dependent transcription in a reporter gene assay (X. Lu, et al. Oncol Rep 19 (2008), pp. 825-830.). Testing a 285 member chemical library derived from planar, aromatic scaffolds in a c-Myc/Max dimerization assay led to identification of four structurally related Myc/Max dimerization inhibitors, which also inhibited DNA binding of c-Myc/Max (Y. Xu, et al. Bioorg Med Chem 14 (2006), pp. 2660-2673.) For example, the compound NY2267 strongly inhibited c-Myc-dependent oncogenic transformation of chicken embryo fibroblasts at 20 μM, showed selectivity over transformation mediated by v-Src or v-Jun, but did not discriminate between transcription mediated by c-Jun and c-Myc. Several compounds were selected from a chemical library on the basis of their ability to prevent association of the HLH-Zip domains of c-Myc and Max in a yeast two-hybrid assay (X. Yin, et al., Oncogene 22 (2003), pp. 6151-6159.). One, 10058-F4 (IC₅₀=49 μM on HL60 cells), served as starting point for the testing of derivatives with improved activities. One of the numerous derivatives resulting from structural variation of the substituents on the aromatic ring and the rhodanine moiety, the compound 28RH-NCN-1, inhibited DNA binding of c-Myc with activity comparable to that of the parent compound, and inhibited growth of HL60 cells with improved potency (IC₅₀=29 μM) (Wang, H., et al., Mol Cancer Ther 6 (2007), pp. 2399-2408). See also PCT/US2007/004039 (WO/2007/098010).

Screening chemical libraries for compounds that inhibited DNA binding of c-Myc, led to discovery of the pyrazolo[1,5-a]pyrimidine Mycro1 (Kiessling, A., et al., Chem Biol 13 (2006), pp. 745-751.). Mycro1 and the derivative Mycro2 were subsequently shown to inhibit c-Myc/Max dimerization, c-Myc-dependent proliferation, gene transcription, and oncogenic transformation. While Mycro1 and Mycro2 displayed good specificities in vitro, they showed only weak-to-moderate specificity for c-Myc-dependent transcription over transcription mediated by AP-1 family proteins, which also dimerize via leucine zippers. A follow-up screen using a focused library of pyrazolo[1,5-a]pyrimidines led to the discovery of the pyrazolo[1,5-fl]pyrimidine 1 (Mycro3), which inhibited c-Myc/Max dimerization and DNA binding with very good selectivity in vitro, and also showed good potency and selectivity at concentrations of 10-40 μM against c-Myc in cellular assays (A. Kiessling, A, et al., Chem Med Chem 2 (2007), pp. 627-630.).

It can be reasoned that inhibitors of the DNA-protein interactions between intact c-Myc/Max dimers and their DNA recognition motif should not interfere with gene transcription repressed by c-Myc, but would still block c-Myc induced transcriptional activation. This distinction can be used to help selectively identify compounds having this mechanism of action. In a screen designed to identify compounds that particularly affect cells with high levels of c-Myc, a compound termed MYRA-A, was discovered, which was shown to inhibit Myc-regulated gene expression, oncogenic transformation, and to induce apoptosis in a Myc-dependent manner (H. Mo and M. Hennksson, Proc Natl Acad Sci USA 103 (2006), pp. 6344-6349.). In a subsequent study, the same group published an additional inhibitor of DNA binding of c-Myc/Max family members dubbed NSC308848 (Mo, H., et al. Cell Cycle 5 (2006), pp. 2191-2194.). Hammoudeh, et al. (2009) identified multiple small molecule binding sites on c-Myc, facilitating use of drug design and/or virtual screening to identify additional c-Myc inhibitors.

Some exemplary small molecule c-Myc inhibitors of use in various embodiments of the invention are shown below. In certain embodiments of the invention analogs of any of these compounds are used.

In some embodiments, a c-Myc inhibitor comprises an RNAi agent (e.g., an siRNA) or an antisense oligonucleotide that inhibits expression of c-Myc. In some embodiments a c-Myc inhibitor comprises an antibody or aptamer that specifically binds to c-Myc.

In some embodiments the agent promotes proteolysis of a polypeptide encoded by an oncogene in a cell (e.g., a tumor cell) exhibiting excessive levels of the cognate transcription factor and more transcriptional coactivator and chromatin regulator occupancy of the super-enhancer then the average single enhancer for the oncogene (e.g., an order of magnitude more). In some embodiments the agent promotes global proteolysis in cell-specific manner such that global proteolysis is only induced in those cells (e.g., tumor cells) exhibiting extremely high levels of the cognate transcription factor of the gene and transcriptional coactivator super-enhancer occupancy. In some embodiments the agent promotes proteolysis of a polypeptide encoded by one or more of a plurality of oncogenes in a cell in which cognate transcription factor levels are high and super-enhancers of the oncogene are occupied by more transcriptional coactivator than the average single enhancer of the oncogene.

The present invention contemplates the use of any agent that is capable of promoting proteolysis. In some embodiments the agent promotes global proteolysis of polypeptides encoded by the oncogenes. In some embodiments the agent promotes global proteolysis of polypeptides encoded by the oncogenes is promoted in cells that exhibit elevated cognate oncogenic transcription factors for the oncogene. In some embodiments the agent promotes global proteolysis of polypeptides is specific to tumor cells that possess oncogenes associated with super-enhancers. In some embodiments the agent promotes global proteolysis of polypeptides in cells that exhibit elevated cognate oncogenic transcription factors and excessive levels of transcriptional co-activator and/or chromatin regulator co-occupancy of super-enhancers and active transcription start sites.

In some embodiments the agent promotes global proteolysis of polypeptides by targeting the oncogene and its expression products for ubiquitin-dependent proteolysis. In some embodiments, the agent promotes global proteolysis of polypeptides by ubiquitin-dependent proteolysis by the proteasome. Ubiquitin-dependent proteolysis is a pathway used by eukaryotic cells for degrading cellular proteins. Protein ubiquitination is catalyzed by the concerted actions of three classes of enzymes; the E1 ubiquitin-activating enzymes, the E2 ubiquitin-conjugating enzymes, and the E3 ubiquitin protein ligases (Hochstrasser, Annu Rev. Genet 30: 405-39, 1996). E1 and E2 are involved in the activation and transfer of ubiquitin, while the substrate specificity of the ubiquitin pathway is conferred by the E3 ubiquitin protein ligases. In some embodiments the agent comprises a ubiquitin protein ligase polypeptide. In some embodiments the agent is an E3 ubiquitin protein ligase polypeptide. In some embodiments the E3 ubiquitin protein ligase is an SCF polypeptide. In some embodiments the agent is a HECT polypeptide. In some embodiments the agent is a UBR1 polypeptide. In some embodiments the E3 ubiquitin protein ligase polypeptide is an F-box polypeptide (e.g., an F-box polypeptide which further comprises a WD domain). In some embodiments the F-box polypeptide is Cdc4p. In some embodiments the F-box polypeptide is Pop1p. In some embodiments the F-box polypeptide is Pop 2p. In some embodiments the F-box polypeptide is Grr1p. In some embodiments the F-box polypeptide is Met30p. In some embodiments the F-box polypeptide is HOSp. In some embodiments the F-box polypeptide is beta TrCPp. In some embodiments the F-box polypeptide is FWD1p. In some embodiments the F-box polypeptide is a polypeptide which is at least 70% identical to a contiguous polypeptide sequence of a polypeptide selected from the group consisting of sequences numbered 2, 4, 6, 8, 10, and 12 in U.S. Pat. No. 7,223,556, which is incorporated herein by reference. In some embodiments the F-box polypeptide is at least 80% identical to a contiguous nucleic acid sequence of sequences numbered 1, 3, 5, 7, 9, and 11 in U.S. Pat. No. 7,223,556, which is incorporated herein by reference.

In some embodiments the agent destabilizes RNA and/or proteins produced by the oncogene. In some embodiments an agent that destabilizes RNA is an agent that modulates nonsense-mediated RNA decay (NMD). Gardner discusses NMD implications for tumorigenesis (Gardner. Mol Cancer Res. 8; 295, 2010). In some embodiments an agent that modulates NMD is an agent that induces NMD of RNA transcripts of cognate oncogenic transcription factors, transcriptional coactivators, or chromatin regulators. In some embodiments an agent that modulates NMD is an agent that downregulates NMD that has been upregulated in a tumor. In some embodiments an agent that modulates NMD is an agent that inhibits Upf1. In some embodiments an agent that inhibits Upf1 is Pateamine A (PatA), as is described by Dang et al. (Dang et al. J Biol Chem. 284(35):23613-21, 2009).

In some embodiments the agent blocks mRNA splicing. In some embodiments an agent that blocks mRNA splicing interferes with alternative splicing. In some embodiments an agent that blocks mRNA splicing is a specific inhibitor of CDC2-like kinase isoforms 1 and 4 (CLK1/CLK4) known as KH-CB19, as is described in Fedorov et al. (Fedorov et al. Chem Biol. 18(1):67-76, 2011). In some embodiments an agent that interferes with alternative spicing is amiloride, as is described by Chang et al. PLos ONE. 6(6):e18643).

In some embodiments an agent that blocks mRNA splicing is an inhibitor of spliceosome catalysis. In some embodiments an agent that inhibits spliceosome catalysis is a 1,4-napthoquinones and/or a 1,4-heterocyclic quinone, non-limiting examples of which are described by Berg et al. (Berg et al. Mol Cell Biol. 32(7):1271-83, 2012). In some embodiments the splicing inhibitor comprises the benzothiazole-4,7-dione, BN82685, which blocks the second of two trans-esterification splicing reactions, preventing the release of intron lariat and exon ligation (Berg et al. 2012). In an embodiment an agent that blocks mRNA splicing comprises 4μ8C, which blocks substrate access to an IRE1 active site and selectively inactivates Xpb1 splicing, as is described by Cross et al. (Cross et al. Proc Natl Acad Sci USA, Epub ahead of print on Feb. 6, 2012).

In some embodiments the agent inhibits translation of mRNA into protein. In some embodiments an agent that inhibits translation of mRNA into protein comprises a nucleoside 5′-monophosphate analog of the mRNA 5′-cap, for example, Barzynkiewics et al. describe nucleotide cap analogs of 7-methylguanosine 5′monophosphate (m7GMP) that acted as competitive inhibitors of capped mRNA translation, including analogs in which the 7-methyl moiety is substituted with 7-ethyl (e7), 7-propyl (p′7), 7-isopropyl (ip7), 7-butyl (b7), 7-isobutyl (ib7), 7-cyclopentyl (cp7), 7-(carboxymethyl) (cm7), 7-benzyle (bn7), 7-(2-phenylethyl) [7-(2-PhEt)], and 7-(1-pentylethyl) [7-(1-PhEt)]. (Darzynkiewics et al. 28(11):4771-8, 1989).

It should be appreciated that the various agents described herein can be used alone, or in combination with other agents described, for example, an agent that interferes with c-Myc enhancer-driven transcription of a plurality of Myc target genes as described in U.S. Application Ser. No. 61/621,897, the entirety of which is hereby incorporated by reference herein.

In some embodiments, an agent is administered in combination with a second therapeutic agent.

In some embodiments, an agent of the present invention is administered in combination with a cancer therapeutic agent. It should be appreciated that the combined administration of an agent of the present invention and a cancer therapeutic agent can be achieved by formulating the cancer therapeutic agent and agent in the same composition or by administering the cancer therapeutic agent and agent separately (e.g., before, after, or interspersed with doses or administration of the cancer therapeutic agent). In some embodiments, an agent of the present invention is administered to a patient undergoing conventional chemotherapy and/or radiotherapy. In some embodiments the cancer therapeutic agent is a chemotherapeutic agent. In some embodiments the cancer therapeutic agent is an immunotherapeutic agent. In some embodiments the cancer therapeutic agent is a radiotherapeutic agent.

Exemplary chemotherapeutic agents that can be administered in combination with the agents of the present invention (e.g., agents that disrupt the function of super-enhancers) include alkylating agents (e.g. cisplatin, carboplatin, oxaloplatin, mechlorethamine, cyclophosphamide, chorambucil, nitrosureas); anti-metabolites (e.g. methotrexate, pemetrexed, 6-mercaptopurine, dacarbazine, fludarabine, 5-fluorouracil, arabinosycytosine, capecitabine, gemcitabine, decitabine); plant alkaloids and terpenoids including vinca alkaloids (e.g. vincristine, vinblastine, vinorelbine), podophyllotoxin (e.g. etoposide, teniposide), taxanes (e.g. paclitaxel, docetaxel); topoisomerase inhibitors (e.g. notecan, topotecan, amasacrine, etoposide phosphate); antitumor antibiotics (dactinomycin, doxorubicin, epirubicin, and bleomycin); ribonucleotides reductase inhibitors; antimicrotubules agents; and retinoids. (See, e.g., Cancer: Principles and Practice of Oncology (V. T. DeVita, et al., eds., J.B. Lippincott Company, 9^(th) ed., 2011; Brunton, L., et al. (eds.) Goodman and Gilman's The Pharmacological Basis of Therapeutics, 12^(th) Ed., McGraw Hill, 2010).

Exemplary immunotherapeutic agents include cytokines, such as, for example interleukin-1 (IL-I), IL-2, IL-4, IL-5, IL-β, IL-7, IL-10, IL-12, IL-I5, IL-18, CSF-GM, CSF-G, IFN-γ, IFN-α, TNF, TGF-β but not limited thereto.

In some embodiments an agent of the present invention can be linked or conjugated to a delivery vehicle, which may also contain cancer therapeutic. Suitable delivery vehicles include liposomes (Hughes et al. Cancer Res 49(22):6214-20, 1989, which is hereby incorporated by reference in its entirety), nanoparticles (Farokhzad et al. Proc Nat'l Acad Sci USA 103(16):6315-20, 2006, which is hereby incorporated by reference in its entirety), biodegradable microspheres, microparticles, and collagen minipellets. The delivery vehicle can contain any of the agents and/or compositions of the present invention, as well as chemotherapeutic, radiotherapeutic, or immunotherapeutic agents described supra.

In some embodiments an agent of the present invention can be conjugated to a liposome delivery vehicle (Sofou and Sgouros, Exp Opin Drug Deliv. 5(2):189-204, 2008, which is hereby incorporated by reference in its entirety). Liposomes are vesicles comprised of one or more concentrically ordered lipid bilayers which encapsulate an aqueous phase. Suitable liposomal delivery vehicles are apparent to those skilled in the art. Different types of liposomes can be prepared according to Bangham et al. J. Mol. Biol. 13:238-52, 1965; U.S. Pat. No. 5,653,996 to Hsu; U.S. Pat. No. 5,643,599 to Lee et al.; U.S. Pat. No. 5,885,613 to Holland et al.; U.S. Pat. No. 5,631,237 to Dzau & Kaneda; and U.S. Pat. No. 5,059,421 to Loughrey et al., which are hereby incorporated by reference in their entirety.

These liposomes can be produced such that they contain, in addition to the therapeutic agents of the present invention, other therapeutic agents, such as immunotherapeutic cytokines, which would then be released at the target site (e.g., Wolff et al., Biochim. Biophys. Acta. 802:259-73, 1984, which is hereby incorporated by reference in its entirety).

The present invention also contemplates a composition comprising an agent of the present invention and a pharmaceutically acceptable carrier, diluent, or excipient. Therapeutic formulations of the agents of the present invention can be prepared having the desired degree of purity with optional pharmaceutically acceptable carriers, excipients or stabilizers (REMINGTON'S PHARMACEUTICAL SCIENCES (A. Osol ed. 1980), which is hereby incorporated by reference in its entirety), in the form of lyophilized formulations or aqueous solutions. Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as acetate, Tris-phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; tonicifiers such as trehalose and sodium chloride; sugars such as sucrose, mannitol, trehalose or sorbitol; surfactant such as polysorbate; salt-forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionic surfactants such as TWEEN®, PLURONICS® or polyethylene glycol (PEG).

The active therapeutic ingredients of the pharmaceutical compositions alone or in combination with or linked to a cancer therapeutic agent or radiotherapeutic agent) can be entrapped in microcapsules prepared using coacervation techniques or by interfacial polymerization, e.g., hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (e.g., liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions. Such techniques are disclosed in REMINGTON'S PHARMACEUTICAL SCIENCES (A. Osol ed. 1980), which is hereby incorporated by reference in its entirety. In some embodiments the agents of the present invention can be conjugated to the microcapsule delivery vehicle to target the delivery of the therapeutic agent to the site of the cells exhibiting super-enhancer associated oncogenes.

Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semi-permeable matrices of solid hydrophobic polymers containing the antibody or polypeptide, which matrices are in the form of shaped articles, e.g., films or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides, copolymers of L-glutamic acid and .gamma. ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOT® (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(−)-3-hydroxybutyric acid.

In some embodiments, an agent of the present invention can be provided with an enteric coating or otherwise protected from hydrolysis or low stomach pH. The therapeutically effective compositions containing the agents of the present invention are administered to a subject, in accordance with known methods, such as intravenous administration, e.g., as a bolus or by continuous infusion over a period of time, by intramuscular, intraperitoneal, intracerobrospinal, subcutaneous, intra-articular, intrasynovial, intrathecal, oral, topical, or inhalation routes.

Other therapeutic regimens may be combined with the administration of the agents of the present invention. The combined administration includes co-administration, using separate formulations or a single pharmaceutical formulation, and consecutive administration in either order, wherein preferably there is a time period while both (or all) active agents simultaneously exert their biological activities. Preferably such combined therapy results in a synergistic therapeutic effect. In some embodiments, a composition of the present invention is administered in combination with a therapy selected from the group consisting of chemotherapy, radiotherapy, proton therapy, surgery, and combinations thereof.

The composition can include any number of additional active ingredients which can act in concert to provide a therapeutic effect, (e.g., a synergistic therapeutic effect), such as a chemotherapeutic agent, a radiotherapeutic agent, a nutritional supplement (e.g. vitamins), an antioxidant, and combinations thereof.

An “effective amount” or “effective dose” of an agent (or composition containing such agent) generally refers to the amount sufficient to achieve a desired biological and/or pharmacological effect, e.g., when contacted with a cell in vitro or administered to a subject according to a selected administration form, route, and/or schedule. As will be appreciated by those of ordinary skill in the art, the absolute amount of a particular agent or composition that is effective may vary depending on such factors as the desired biological or pharmacological endpoint, the agent to be delivered, the target tissue, etc. Those of ordinary skill in the art will further understand that an “effective amount” may be contacted with cells or administered in a single dose, or through use of multiple doses, in various embodiments. It will be understood that agents, compounds, and compositions herein may be employed in an amount effective to achieve a desired biological and/or therapeutic effect.

In certain aspects, the present invention relates to a method of treating a proliferative disorder in a patient in need of such treatment, said proliferative disorder characterized by an oncogene-associated super-enhancer occupied by more Mediator or BRD4 than an average single enhancer, comprising administering to the patient an effective amount of an agent that disrupts the function of the oncogene-associated super-enhancer, thereby selectively inhibiting proliferation of the oncogene in the patient.

It should be apparent to those skilled in the art that any of the compounds or agents described above can be employed in the method of treating the disorder (e.g., a proliferative disorder) to achieve the desired result of disrupting the function of the super-enhancer.

The present invention contemplates the treatment of any proliferative disorder (e.g., cancer) that is characterized by an oncogene-associated super-enhancer. In some embodiments, the invention includes the treatment of a disorder (e.g., a proliferative disorder such as cancer) that is characterized by an gene-associated super-enhancer wherein the gene is a gene associate with a hallmark of the disease such as cancer. In some embodiments, the proliferative disorder to be treated is a hematological malignancy. In some embodiments, the proliferative disorder to be treated is selected from the group consisting of acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), chronic lymphocytic leukemia (CLL), hairy cell leukemia, Hodgkin's lymphoma, non-Hodgkin's lymphoma, cutaneous T-cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), Mantle cell lymphoma, B-cell lymphoma, acute lymphoblastic T cell leukemia (T-ALL), acute promyelocytic leukemia, and multiple myeloma. In some embodiments, the proliferative disorder is a non-hematological malignancy.

In certain exemplary embodiments, the agent is a BRD4 inhibitor, for example, small molecule JQ1 or iBET.

In some aspects, the present invention relates to a method of treating multiple myeloma involving an IGH-MYC locus that results in aberrant expression of oncogene c-Myc, comprising administering to a patient in need of such treatment an effective amount of an agent that decreases occupancy levels of BRD4 and MED1 at a super-enhancer associated with the IGH-MYC locus, wherein decreased occupancy levels of BRD4 and MED1 at the super-enhancer disrupt function of the super-enhancer thereby decreasing aberrant expression of oncogene c-Myc such that the multiple myeloma is treated. In some embodiments, the agent is a BRD4 inhibitor, for example, JQ1 or iBET.

In some aspects, the present invention relates to a method of identifying an agent that disrupts a super-enhancer associated with a gene, comprising: (a) providing a cell or cell free system comprising a super-enhancer, or functional fragment and/or variant thereof, and an associated gene, e.g., a reporter gene; (b) contacting the cell with a test agent, e.g., under conditions suitable for the super-enhancer to drive expression of the associated gene, e.g., to drive expression at a preselected level, e.g., a high level; (c) and measuring the level of expression of the associated gene.

In an embodiment decreased expression of the associated gene in the presence of the test agent indicates that the test agent is as an agent that disrupts the super-enhancer associated with the gene.

In an embodiment the method comprises transfecting a cell with a super-enhancer and the associated gene under conditions suitable for the super-enhancer to drive high levels of expression of the associated gene.

In an embodiment the method comprises comparing the level of expression with a reference, e.g., expression in a similar system not contacted with the test agent.

In an embodiment the method comprises confirming disruption of the super-enhancer, or functional fragment and/or variant thereof, e.g., by analysis of the presence of one or more super-enhancer component.

In an embodiment the method is first performed in a cell-free system and repeated in cell preparation, e.g., a cultured cell.

In an embodiment the method is first performed in a cell-free system or a cell preparation, e.g., a cultured cell, and repeated in an animal.

In an embodiment the super-enhancer is associated with a gene that is expressed in a disease state cell, e.g., a cancer cell.

In an embodiment the method comprises memorializing the results.

A wide variety of test agents can be used in the methods. For example, a test agent can be a small molecule, polypeptide, peptide, nucleic acid, oligonucleotide, lipid, carbohydrate, or hybrid molecule. Compounds can be obtained from natural sources or produced synthetically. Compounds can be at least partially pure or may be present in extracts or other types of mixtures. Extracts or fractions thereof can be produced from, e.g., plants, animals, microorganisms, marine organisms, fermentation broths (e.g., soil, bacterial or fungal fermentation broths), etc. In some embodiments, a compound collection (“library”) is tested. The library may comprise, e.g., between 100 and 500,000 compounds, or more. Compounds are often arrayed in multiwell plates. They can be dissolved in a solvent (e.g., DMSO) or provided in dry form, e.g., as a powder or solid. Collections of synthetic, semi-synthetic, and/or naturally occurring compounds can be tested. Compound libraries can comprise structurally related, structurally diverse, or structurally unrelated compounds. Compounds may be artificial (having a structure invented by man and not found in nature) or naturally occurring. In some embodiments a library comprises at least some compounds that have been identified as “hits” or “leads” in other drug discovery programs and/or derivatives thereof. A compound library can comprise natural products and/or compounds generated using non-directed or directed synthetic organic chemistry. Often a compound library is a small molecule library. Other libraries of interest include peptide or peptoid libraries, cDNA libraries, and oligonucleotide libraries. A library can be focused (e.g., composed primarily of compounds having the same core structure, derived from the same precursor, or having at least one biochemical activity in common).

Compound libraries are available from a number of commercial vendors such as Tocris BioScience, Nanosyn, BioFocus, and from government entities. For example, the Molecular Libraries Small Molecule Repository (MLSMR), a component of the U.S. National Institutes of Health (NIH) Molecular Libraries Program is designed to identify, acquire, maintain, and distribute a collection of >300,000 chemically diverse compounds with known and unknown biological activities for use, e.g., in high-throughput screening (HTS) assays (see https://mli.nih.gov/mli/). The NIH Clinical Collection (NCC) is a plated array of approximately 450 small molecules that have a history of use in human clinical trials. These compounds are highly drug-like with known safety profiles. The NCC collection is arrayed in six 96-well plates. 50 μl of each compound is supplied, as an approximately 10 mM solution in 100% DMSO. In some embodiments, a collection of compounds comprising “approved human drugs” is tested. An “approved human drug” is a compound that has been approved for use in treating humans by a government regulatory agency such as the US Food and Drug Administration, European Medicines Evaluation Agency, or a similar agency responsible for evaluating at least the safety of therapeutic agents prior to allowing them to be marketed. The test agent may be, e.g., an antineoplastic, antibacterial, antiviral, antifungal, antiprotozoal, antiparasitic, antidepressant, antipsychotic, anesthetic, antianginal, antihypertensive, antiarrhythmic, antiinflammatory, analgesic, antithrombotic, antiemetic, immunomodulator, antidiabetic, lipid- or cholesterol-lowering (e.g., statin), anticonvulsant, anticoagulant, antianxiety, hypnotic (sleep-inducing), hormonal, or anti-hormonal drug, etc. In some embodiments, a compound is one that has undergone at least some preclinical or clinical development or has been determined or predicted to have “drug-like” properties. For example, the test agent may have completed a Phase I trial or at least a preclinical study in non-human animals and shown evidence of safety and tolerability. In some embodiments, a test agent is substantially non-toxic to cells of an organism to which the compound may be administered or cells in which the compound may be tested, at the concentration to be used or, in some embodiments, at concentrations up to 10-fold, 100-fold, or 1,000-fold higher than the concentration to be used. For example, there may be no statistically significant adverse effect on cell viability and/or proliferation, or the reduction in viability or proliferation can be no more than 1%, 5%, or 10% in various embodiments.

In various embodiments of any aspect herein pertaining to screening methods (e.g., methods of identifying agents), the screen may be performed using a single test agent or multiple test agents in a given reaction vessel. In various embodiments the number of reaction vessels and/or test agents is at least 10; 100; 1000; 10,000; 100,000, or more. In some embodiments of any aspect herein pertaining at least in part to screening methods (e.g., methods of identifying agents) a high throughput screen (HTS) is performed. High throughput screens often involve testing large numbers of test agents with high efficiency, e.g., in parallel. For example, tens or hundreds of thousands of agents may be routinely screened in short periods of time, e.g., hours to days. Such screening is often performed in multiwell plates (sometimes referred to as microwell or microtiter plates or microplates) containing, e.g., 96, 384, 1536, 3456, or more wells or other vessels in which multiple physically separated depressions, wells, cavities, or areas (collectively “wells”) are present in or on a substrate. Different test agent(s) may be present in or added to the different wells. It will be understood that some wells may be empty, may comprise replicates, or may contain control agents or vehicle. High throughput screens may involve use of automation, e.g., for liquid handling, imaging, and/or data acquisition or processing, etc. In some embodiments an integrated robot system comprising one or more robots transports assay-microplates from station to station for, e.g., addition, mixing, and/or incubation of assay constituents (e.g., test agent, target, substrate) and, in some embodiments, readout or detection. A HTS system may prepare, incubate, and analyze many plates simultaneously. Certain general principles and techniques that may be applied in embodiments of a HTS are described in Macarrón R & Hertzberg R P. Design and implementation of high-throughput screening assays. Methods Mol Biol., 565:1-32, 2009 and/or An W F & Tolliday N J., Introduction: cell-based assays for high-throughput screening. Methods Mol Biol. 486:1-12, 2009, and/or references in either of these. Exemplary methods are also disclosed in High Throughput Screening: Methods and Protocols (Methods in Molecular Biology) by William P. Janzen (2002) and High-Throughput Screening in Drug Discovery (Methods and Principles in Medicinal Chemistry) (2006) by Jorg H{umlaut over (υ)}ser. Test agent(s) showing an activity of interest (sometimes termed “hits”) may be retested and/or, optionally (e.g., depending at least in part on results of retesting) selected for further testing, development, or use. In some embodiments one or more structural analogs of a hit is synthesized. Such analogs may, for example, comprise substitution of one or more functional groups or heteroatoms present in the hit by a different functional group or heteroatom or substituting a heteroatom or functional group present in place of a hydrogen in the hit, etc. In some embodiments one or more such analog(s) are then tested for a property or activity of interest (e.g., ability to disrupt a super-enhancer associated with an oncogene or disease related gene).

Positive and/or negative controls may be used in any of the screens. An appropriate positive or negative control can be selected based at least in part on the assay. A negative control may be to perform the assay in the absence of a test agent.

In some embodiments, information derived from sequence analysis, mutational analysis, and/or structural analysis is used in the identification of a modulator, e.g., an agent that interferes with transcriptional coactivator or BRD4 co-occupancy of super-enhancers and active transcription start sites. For example, in some embodiments a structure (e.g., a two-dimensional or three-dimensional structure) of a target, e.g., a TF, generated at least in part using, e.g., nuclear magnetic resonance, homology modeling, and/or X-ray crystallography is used. In some embodiments a structure obtained with a ligand (e.g., an inhibitor) bound to the target may be used. In some embodiments a computer-aided computational approach sometimes referred to as “virtual screening” is used in the identification of candidate modulators. Structures of compounds, e.g., small molecules may be screened for ability to bind to a region (e.g., a “pocket”) accessible to the compound. The region may be any region accessible to the compound, e.g., a concave region on the surface or a cleft or a region involved in dimerization. A variety of docking and pharmacophore-based algorithms are known in the art, and computer programs implementing such algorithms are available. Commonly used programs include Gold, Dock, Glide, FlexX, Fred, and LigandFit (including the most recent releases thereof). See, e.g., Ghosh, S., et al., Current Opinion in Chemical Biology, 10(3): 194-2-2, 2006; McInnes C., Current Opinion in Chemical Biology; 11(5): 494-502, 2007, and references in either of the foregoing articles, which are incorporated herein by reference. In some embodiments a virtual screening algorithm may involve two major phases: searching (also called “docking”) and scoring. During the first phase, the program automatically generates a set of candidate complexes of two molecules (test compound and target molecule) and determines the energy of interaction of the candidate complexes. The scoring phase assigns scores to the candidate complexes and selects a structure that displays favorable interactions based at least in part on the energy. To perform virtual screening, this process may be repeated with a large number of test compounds to identify those that, for example, display the most favorable interactions with the target. In some embodiments, low-energy binding modes of a small molecule within an active site or possible active site or other target region are identified. In some embodiments a compound capable of docking at a site where mutations are known to inhibit activity of the target is identified. Variations may include the use of rigid or flexible docking algorithms and/or including the potential binding of water molecules. In some embodiments the three-dimensional structure of an enzyme's active site may be used to identify potential inhibitors. Agent(s) that have the potential to bind in or near an active site may be identified. These predictions may then be tested using the actual compound. A new inhibitor thus identified may then be used to obtain a structure of the enzyme in an inhibitor/enzyme complex to show how the molecule is binding to the active site. Further changes may be made to the inhibitor, e.g., to try to improve binding. This cycle may be repeated until an inhibitor of sufficient predicted or actual potency (e.g., a desired potency for therapeutic purposes) is identified. Numerous small molecule structures are available and can be used for virtual screening. A collection of compound structures may sometimes referred to as a “virtual library”. For example, ZINC is a publicly available database containing structures of millions of commercially available compounds that can be used for virtual screening (http://zinc.docking.org/; Shoichet, J. Chem. Inf. Model., 45(1):177-82, 2005). A database containing about 250,000 small molecule structures is available on the National Cancer Institute (U.S.) website (at http://129.43.27.140/ncidb2/). In some embodiments multiple small molecules may be screened, e.g., up to 50,000; 100,000; 250,000; 500,000, or up to 1 million, 2 million, 5 million, 10 million, or more. Compounds can be scored and, optionally, ranked by their potential to bind to a target. Compounds identified in virtual screens can be tested in cell-free or cell-based assays or in animal models to confirm their ability to inhibit activity of a target molecule, their ability to activate a target molecule, and/or to assess their biological and/or pharmacological activity. Computational approaches may be used to predict one or more physico-chemical, pharmacokinetic and/or pharmacodynamic properties of compounds identified in a physical or virtual screen. Such information may be used, e.g., to select one or more hits for, e.g., further testing, development, or use. For example, small molecules having characteristics typical of “drug-like” molecules may be selected and/or small molecules having one or more undesired characteristics may be avoided.

In some aspects of any screening and/or characterization methods, test agents are contacted with test cells (and optionally control cells) or used in cell-free assays at a predetermined concentration. In some embodiment the concentration is about up to 1 nM. In some embodiments the concentration is between about 1 nM and about 100 nM. In some embodiments the concentration is between about 100 nM and about 10 μM. In some embodiments the concentration is at or above 10 μM, e.g., between 10 μM and 100 μM. Following incubation for an appropriate time, optionally a predetermined time, the effect of compounds or composition on a parameter of interest in the test cells is determined by an appropriate method known to one of ordinary skill in the art, e.g., as described herein. Cells can be contacted with compounds for various periods of time. In certain embodiments cells are contacted for between 12 hours and 20 days, e.g., for between 1 and 10 days, for between 2 and 5 days, or any intervening range or particular value. Cells can be contacted transiently or continuously. If desired, the compound can be removed prior to assessing the effect on the cells.

One skilled in the art readily appreciates that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The details of the description and the examples herein are representative of certain embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Modifications therein and other uses will occur to those skilled in the art. These modifications are encompassed within the spirit of the invention. It will be readily apparent to a person skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention.

The articles “a” and “an” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to include the plural referents. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention also includes embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process. Furthermore, it is to be understood that the invention provides all variations, combinations, and permutations in which one or more limitations, elements, clauses, descriptive terms, etc., from one or more of the listed claims is introduced into another claim dependent on the same base claim (or, as relevant, any other claim) unless otherwise indicated or unless it would be evident to one of ordinary skill in the art that a contradiction or inconsistency would arise. It is contemplated that all embodiments described herein are applicable to all different aspects of the invention where appropriate. It is also contemplated that any of the embodiments or aspects can be freely combined with one or more other such embodiments or aspects whenever appropriate. Where elements are presented as lists, e.g., in Markush group or similar format, it is to be understood that each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements, features, etc., certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements, features, etc. For purposes of simplicity those embodiments have not in every case been specifically set forth in so many words herein. It should also be understood that any embodiment or aspect of the invention can be explicitly excluded from the claims, regardless of whether the specific exclusion is recited in the specification. For example, any one or more nucleic acids, polypeptides, cells, species or types of organism, disorders, subjects, or combinations thereof, can be excluded.

Where the claims or description relate to a composition of matter, e.g., a nucleic acid, polypeptide, cell, or non-human transgenic animal, it is to be understood that methods of making or using the composition of matter according to any of the methods disclosed herein, and methods of using the composition of matter for any of the purposes disclosed herein are aspects of the invention, unless otherwise indicated or unless it would be evident to one of ordinary skill in the art that a contradiction or inconsistency would arise. Where the claims or description relate to a method, e.g., it is to be understood that methods of making compositions useful for performing the method, and products produced according to the method, are aspects of the invention, unless otherwise indicated or unless it would be evident to one of ordinary skill in the art that a contradiction or inconsistency would arise.

Where ranges are given herein, the invention includes embodiments in which the endpoints are included, embodiments in which both endpoints are excluded, and embodiments in which one endpoint is included and the other is excluded. It should be assumed that both endpoints are included unless indicated otherwise. Furthermore, it is to be understood that unless otherwise indicated or otherwise evident from the context and understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value or subrange within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise. It is also understood that where a series of numerical values is stated herein, the invention includes embodiments that relate analogously to any intervening value or range defined by any two values in the series, and that the lowest value may be taken as a minimum and the greatest value may be taken as a maximum. Numerical values, as used herein, include values expressed as percentages. For any embodiment of the invention in which a numerical value is prefaced by “about” or “approximately”, the invention includes an embodiment in which the exact value is recited. For any embodiment of the invention in which a numerical value is not prefaced by “about” or “approximately”, the invention includes an embodiment in which the value is prefaced by “about” or “approximately”. “Approximately” or “about” generally includes numbers that fall within a range of 1% or in some embodiments within a range of 5% of a number or in some embodiments within a range of 10% of a number in either direction (greater than or less than the number) unless otherwise stated or otherwise evident from the context (except where such number would impermissibly exceed 100% of a possible value). It should be understood that, unless clearly indicated to the contrary, in any methods claimed herein that include more than one act, the order of the acts of the method is not necessarily limited to the order in which the acts of the method are recited, but the invention includes embodiments in which the order is so limited. It should also be understood that unless otherwise indicated or evident from the context, any product or composition described herein may be considered “isolated”.

EXAMPLES Example 1 Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes Introduction

Transcription factors typically regulate gene expression by binding cis-acting regulatory elements known as enhancers and recruiting coactivators and RNA Polymerase II (RNA Pol II) to target genes (Ong and Corces, 2011). Transcription factor-bound enhancers interact with target gene promoters via DNA looping events facilitated by the Mediator co-activator complex and cohesin (Kagey et al., 2010). Between 400,000 and 1.4 million putative enhancers have been identified in the mammalian genome (Bernstein et al., 2012; Thurman et al., 2012). In any one cell type, the number of active enhancers is estimated to be in the thousands and enhancer activity is largely cell-type specific (Bernstein et al., 2012; Shen et al., 2012; Yip et al., 2012). Whereas most genes are transcriptionally active in multiple cell types, enhancers tend to be active only in specific lineages (Shen et al., 2012). These data suggest that much of the transcriptional control of mammalian development is due to the diverse activity of enhancers that control cell type specific patterns of gene expression.

In embryonic stem cells (ESCs), control of the gene expression program that establishes and maintains ESC state is dependent on a remarkably small number of master transcription factors (Young, 2011). These transcription factors, which include Oct4, Sox2 and Nanog (OSN), bind to approximately 7,000 enhancers together with the Mediator coactivator complex (Kagey et al., 2010). The Mediator complex facilitates the ability of enhancer-bound transcription factors to recruit RNA Pol II to the promoters of target genes (Malik and Roeder, 2010) and is essential for maintenance of ESC state and early embryonic development (Kagey et al., 2010). Reduced levels of either Oct4 or Mediator have a very similar effect on the ESC gene expression program and cause the same rapid loss of ESC identity (Kagey et al., 2010).

It is striking that ESC maintenance is highly sensitive to perturbations in the levels of Mediator (Kagey et al., 2010). To understand the reasons underlying this hypersensitivity, we investigated enhancers bound by Mediator in these cells. We identified approximately 200 genomic regions that contained tightly spaced clusters of enhancers spanning extraordinarily large domains. These “super-enhancers” were occupied by an order of magnitude more Mediator than the average enhancer, and were associated with the key cell-type specific ESC genes. These enhancers also conferred stronger enhancer activity relative to the average enhancer, suggesting these elements drive gene expression programs and cell state. During ESC differentiation, the ESC super-enhancers were rapidly lost and new super-enhancers were formed at genes key to the differentiated cell type. Additional cell types were found to have super-enhancers associated with highly expressed and cell-type specific genes. These results argue that super-enhancers drive genes essential for cell identity in multiple cell types and that these elements are especially sensitive to perturbations involved in dynamic changes in cell state.

Results Large Genomic Domains Occupied by Mediator in ESCs

Previous studies have shown that co-occupancy of sites by the Oct4, Sox2 and Nanog transcription factors is highly predictive of enhancer activity (Chen et al., 2008). We generated ChIP-Seq data for Oct4, Sox2, Nanog (OSN) in murine ESCs and identified 6,343 regions that were bound by all three transcription factors. The Mediator co-activator complex has been previously shown to interact with the enhancer-bound transcription factors and facilitate recruitment of the transcription apparatus to active gene promoters (Malik and Roeder, 2010). Analysis of the 6,343 OSN regions confirmed the presence of Mediator, including regions surrounding the Klf4 gene (FIG. 1A). Therefore, we defined the 6,343 regions bound by OSN as ESC enhancers.

Closer inspection of the 6,343 ESC enhancers revealed a surprising feature: some ESC enhancers are occupied by extremely high levels of Mediator (FIG. 1B). Global analysis of the 6,343 ESC enhancers confirmed the distribution of Mediator occupancy across this set of regions is not evenly distributed (FIG. 1C). Instead, there is a distribution of occupancy that indicates these regions fall into two distinct classes, with one class containing an exceptional amount of Mediator proteins (FIG. 1C). Further analysis of this small subset (211) of regions revealed that, on average, they contained 27 times more Mediator proteins compared to the remaining 6,132 enhancers (FIG. 1D). Additionally, on average these regions covered larger genomic distances (5.2 kb) compared to the remaining enhancers (469 bp) (FIG. 1D). Thus, these ˜200 regions, which we call “super-enhancers”, are occupied by at least an order of magnitude more Mediator relative to the mean, and typically span DNA domains at least an order of magnitude larger.

Many genome wide enhancer mapping efforts utilize histone marks and regulatory proteins as surrogates for enhancers (Bernstein et al., 2012; Shen et al., 2012). Further characterization of the super-enhancers revealed that these regions are also occupied by other enhancer-associated modifications and proteins, including H3K27ac, a histone modification commonly found at enhancers and used to predict regions of enhancers activity (Creyghton et al., 2010; Rada-Iglesias et al., 2011). Interestingly, H3K27Ac failed to reveal the striking disparity noted for OSN-Mediator bound super-enhancers. Thus, Mediator ChIP-Seq data is superior to surrogate data from histone modifications for identifying super-enhancers in ESCs.

Super-Enhancers are Associated with Key ESC Genes

Most studies have assigned enhancers to putative target genes by using the proximity of enhancers and target genes. Recent work has identified topological domains associated with transcriptional control in the ESC genome using high throughput chromatin conformation capture data (Hi-C) (Dixon et al., 2012). We therefore used proximity of enhancer elements and genes to facilitate mapping of ESC enhancers to promoters, and further used Hi-C to additionally assign enhancers to promoters of genes that were greater than 40 kb away. Previous studies using chromatin configuration capture (3C) have shown that, at an enhancer element brought into close proximity to a promoter region by DNA looping, the Mediator ChIP-Seq signals are similar at both regions (Kagey et al., 2010). We therefore required that enhancer-promoter interaction candidates have similar levels of Mediator. The assignments of super-enhancers to promoters identified 192 genes, with a further 5,300 assigned by Hi-C. For three of these genes, the proximity between portions of the super-enhancer and the target promoter were previously established using 3C (Kagey et al., 2010).

A global RNA sequencing (RNA-Seq) analysis of the genes assigned to ESC enhancers confirmed that these genes were expressed at very high levels compared to other genes in ESCs (FIG. 2A). Further examination of this set of genes, however, revealed a striking difference: the super-enhancer-associated genes were expressed at higher levels compared to those neighboring the remaining enhancers (FIG. 2B,C). Compared to the average expression levels of genes near the median enhancer (1.84 RPKM), genes associated with super-enhancers were expressed 6-times higher (FIG. 2A). These results suggest super-enhancers are associated with the most highly expressed genes compared to other enhancers.

We next determined if these highly expressed genes were important for ESC identity. In contrast to the other highly expressed genes that were found near the 6,132 enhancers, including house-keeping genes, super-enhancer-associated genes are critical for ESC maintenance and reprogramming. Super-enhancers were directly associated with many genes previously shown to play important roles in ESC identity, including Esrrb (Ivanova et al., 2006; Zhang et al., 2008); Tbx3 (Ivanova et al., 2006; Niwa et al., 2009); and the mir290-295 microRNA gene cluster (Lichner et al., 2011; Marson et al., 2008; Zovoilis et al., 2009). Remarkably, the super-enhancer-associated genes included those encoding the ESC master transcription factors Oct4, Sox2 and Nanog (FIG. 2D). These three transcription factors are known to auto-regulate their expression through promoter binding, forming an interconnected autoregulatory loop. This form of auto-regulation is a core feature of the ESC transcriptional regulatory circuitry (Boyer et al., 2005), whose establishment is likely key to reprogramming of various cells into iPS cells (Jaenisch and Young, 2008). Small portions of the super-enhancers associated with these genes have previously been shown to have enhancer activity in reporter assays (Chen et al., 2008) and to participate in enhancer-promoter looping at the Oct4 and Nanog genes (Kagey et al., 2010). Thus, the genes encoding the master transcription factors are themselves under the control of super-enhancers. Overall these results support a model that super-enhancers associate with highly expressed and highly cell-type specific genes that include key drivers of ESC identity.

Super-Enhancers Confer Strong Enhancer Activity

One striking feature of the super-enhancers is that they contain multiple, highly enriched regions of Mediator compared to average enhancers that typically consist of a single peak of the coactivator (FIG. 3A). DNA sequence analysis confirmed that super-enhancers contained more OSN binding motifs than do median enhancers (FIG. 3A). To test whether these super-enhancers confer stronger enhancer activity than median enhancers, we cloned 3 kb regions of super-enhancers and median enhancers into luciferase reporter constructs that were subsequently transfected into ESCs. We found that on average, super-enhancers drove 16 times more luciferase expression than median enhancers (FIG. 3B). Since a super-enhancer contained more Mediator occupancy compared to a median enhancer, these results suggested that clusters of enhancers may display higher enhancer activity in ESCs. To test this model, we generated an artificial super-enhancer by oligomerizing the distal median enhancer of the Sgk1 gene. As a single median enhancer, this region displayed low luciferase activity (FIG. 3B). Remarkably, the dimeric Sgk1 enhancer exhibited 2-times higher activity, while the tetrameric Sgk1 enhancer exhibited 3-times higher enhancer activity compared to the single Sgk1 enhancer driving luciferase expression in ESCs (FIG. 3C). These results suggest that super-enhancers can be formed by clusters of enhancers, that they have higher activity than median enhancers, and are sufficient to drive high expression of key, cell type-specific genes required to maintain ESC identity.

Rapid Loss of ESC Super-Enhancers During ESC Differentiation

If super-enhancers play key roles in transcriptional control of cell identity, then differentiation of ESCs should lead to loss of ESC super-enhancers. To test this notion, we stimulated ESCs to differentiate into a trophectoderm lineage by shutting down Oct4 transcription (FIG. 4A)(Niwa et al., 2000). Loss of Oct4 results in cellular differentiation, loss of expression of Oct4 target genes, and upregulation of the trophectoderm master regulator transcription factor Cdx2 (Deb et al., 2006; Niwa et al., 2005; Strumpf et al., 2005; Wang et al., 2010).

The fate of ESC super-enhancers during differentiation was examined by profiling global levels of Mediator using ChIP-PCR (FIG. 4B). All seven of the super-enhancers tested that were occupied by OSN and Mediator in ESCs had at least two-fold lower levels of Mediator proteins upon differentiation (FIG. 4B). On average, the tested super-enhancers had 68% lower levels of Mediator upon ESC differentiation compared to control ESCs (FIG. 4B). This included the super-enhancers to the key ESC genes Oct4/Pou5f1 and Sox2 (FIG. 4B). In contrast, four of the five typical enhancers that were tested retained high levels of Mediator compared to super-enhancers upon ESC differentiation (FIG. 4B). Surprisingly, only one of the typical enhancers tested had at least two-fold lower levels of Mediator upon differentiation (FIG. 4B). On average, median enhancers had only 14% lower levels of Mediator upon differentiation compared to control ESCs (FIG. 4B). Together, these results are consistent with the model that super-enhancers play key roles in establishing and maintaining cell state, and that these enhancer elements are sensitive to perturbations that accompany the dynamic changes in cell state during differentiation.

Super-Enhancers are Found in Multiple Cell Types and are Cell-Type Specific

The identification of both ESC and trophectoderm lineage super-enhancers suggest that super-enhancers may be a common feature of mammalian cells. Accordingly, in any given cell type, super-enhancer associated genes are likely to play prominent roles in establishing and maintaining cell identity. Further, the pattern of super-enhancers in any given cell type is likely to be cell-type specific.

To test these predictions, we profiled Mediator levels and master transcription factor Pu.1 in pro-B cells using ChIP-Seq. Mediator occupancy highly correlated with occupancy of Pu.1 at promoter distal sites (FIG. 5A, B). Of the 13,303 sites bound by Pu.1 in pro-B cells, 79% were co-occupied by Mediator. Using similar criteria as in ESCs, 392 super-enhancers were identified in pro-B cells, and exhibited extremely high levels of Mediator occupancy (FIG. 5B,C). On average, the pro-B super-enhancers contained 31 times more Mediator proteins compared to the remaining 12,911 enhancers, and covered larger genomic distances (15.4 kb) compared to the remaining enhancers (422 bp). These findings support the conclusion that super-enhancers are a general feature of mammalian cells.

Genes associated with super-enhancers in pro-B cells were previously shown to be important for pro-B cell development, supporting the model that super-enhancers drive expression of target genes critical for cellular identity. Among the 355 super-enhancer-associated genes that are highly expressed in pro-B cells included many genes previously shown to play important roles in B cell development, including Pax5; Rag2; VpreB1 and VpreB2. We next determined if super-enhancers and their associated genes are cell-type specific by comparing ESC and pro-B cell super-enhancers and their target genes (FIG. 5D,E). The set of super-enhancers showed minimal overlap between ESCs and pro-B cells (FIG. 5D). Of the 211 ESC super-enhancers, only 9 regions (2%) overlapped with the pro-B cell super-enhancers (FIG. 5D). Furthermore, the super-enhancer-associated genes exhibited highly cell-type specific patterns of expression (FIG. 5D). Of the 192 genes neighboring super-enhancers in ESCs, only 15 (8%) were associated with super-enhancers in pro-B cells (FIG. 5E). These results suggest that super-enhancers are likely to be a general feature of most cell types and are likely to drive the expression of genes controlling cellular identity.

Discussion

We have identified in multiple cell types the existence of super-enhancers. Super-enhancers are enhancers bound by master regulator transcription factors that contain disproportionately high levels of the Mediator co-activator complex. Mediator levels are likely to be rate limiting for enhancer mediated transcription and as such, the disparity in Mediator levels at super-enhancers potentially represents an important hierarchical stratification of enhancers. Indeed, in multiple cell types, super-enhancers associate with known genes essential for cell identity and globally are likely to be the drivers of key cell identity controlling genes.

The observation of super-enhancers also suggests the complexity of cis-regulating elements can be significantly reduced. Although somewhere between hundreds of thousand and millions of enhancers are likely to exist in the mammalian genome, in any given cell type only a few hundred super-enhancers are likely to drive the expression of genes that establish cellular identity. In many cell types, small subsets of transcriptionally active genes have been identified through genetic screens as essential for cellular identity. However an analogous appreciation does not exist for enhancers in any given cell types. The characteristic features of super-enhancers strongly suggest that they may be among the most essential enhancers in any given cell type.

Lastly, the ability of super-enhancers to drive expression of key cell identity genes suggest that mutations to super-enhancers may potentially lead to disease and developmental defect. Indeed, recent evidence from the ENCODE consortium revealed that the majority of disease associated SNPs occur in regulatory regions (Bernstein et al., 2012; Schaub et al., 2012). It is easy to imagine that loss of a super-enhancer through genetic deletions could lead to developmental defects through the inability to fully establish cellular identity. Conversely, translocation of a super-enhancer could result in aberrant gene regulation. Example 2 below provides evidence that super-enhancers associate with key cancer dependency genes, including c-Myc via the translocated IgH super-enhancer in Multiple Myeloma.

The association of super-enhancers with key cell identity genes as well as cancer dependency genes argues that super-enhancers are important and essential components of cellular identity. Given super-enhancers reflect the occupancy of master regulator transcription factors in a given cell type, identification of super-enhancers in any cell type could potentially facilitate the mapping of the core transcriptional circuitry. In disease cells, super-enhancers have the potential to act as powerful biomarkers, identifiers of drug target candidates, and can potentially they themselves be drugged via targeting of Mediator and other enhancer bound components. More importantly, the characterization of super-enhancers implores a departure from a gene centric view of the genome, and instead supports an appreciation that regulatory control regions found in intergenic DNA may represent key features in the blueprints of mammalian development and disease.

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Example 2 Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers Introduction

Inhibitors of chromatin regulators are gaining interest as therapeutic agents for cancer because of their ability to specifically repress key oncogenic drivers in many tumor types. A major challenge in cancer therapeutics has been the direct pharmacologic inhibition of oncogenic transcription factors such as c-MYC. MYC is one of the most commonly amplified oncogenes in cancer, but lacks clear ligand-binding domains, rendering it difficult to target by small molecule inhibitors (Nair and Burley, 2003). However, several recent studies have shown that inhibition of chromatin regulators, such as the bromodomain protein BRD4, may represent an alternate avenue for selectively targeting these key oncogenic drivers. It is not yet known how inhibition of a general transcriptional regulator can exert a specific effect on a small number of genes. Understanding this concept will aid the development and selection of drugs in treating many cancers.

BRD4 was first identified as an interaction partner of the murine Mediator coactivator complex, and has subsequently been shown to associate with this transcription complex in a variety of human cells (Dawson et al., 2011; Jiang et al., 1998; Wu et al., 2003). BRD4 is also involved in the control of transcriptional elongation through its association with the positive transcription elongation factor, P-TEFb (Jang et al., 2005; Yang et al., 2005). In addition, bromodomain proteins can associate with specific acetylated histone residues, an interaction which can be disrupted by small molecules that competitively occupy the acetyl-lysing binding pockets in select members of this 61-member protein family (Filippakopoulos et al., 2012). Two recently developed bromodomain inhibitors, JQ1 and iBET, selectively bind to BRD4 (Filippakopoulos et al., 2010; Nicodeme et al., 2010). Despite this general role played in transcription regulation, inhibition of BRD4 by BET-inhibitors appears to have a highly selective effect on tumor cells (Dawson et al., 2011; Delmore et al., 2011; Mertz et al., 2011; Zuber et al., 2011). BET-inhibitors appear to cause dramatic suppression of the potent oncogene, MYC, and lead to a pronounced antiproliferative effect in a range of tumors, including multiple myeloma (MM), Burkitt's lymphoma (BL), and acute myeloid leukemia (AML) (Dawson et al., 2011; Delmore et al., 2011; Mertz et al., 2011; Zuber et al., 2011). Although BRD4 inhibition shows great promise as a therapeutic agent in cancer, it remains unclear why inhibition of this general chromatin regulator has a selective effect on the MYC gene in these tumor cells.

To investigate this mechanism, we turned to concepts described Example 1 above. In that study, we demonstrated that transcriptional activators, such as the Mediator coactivator complex are not distributed evenly throughout the genome. Instead, we found that Mediator binding is concentrated at a discrete number of enhancer regions, which we have classified as super-enhancers. Our analysis of mouse embryonic stem cells (mESCs) revealed that these “super-enhancers” consist of enhancer clusters that span vast chromatin domains when compared to typical enhancer regions and are occupied by an order of magnitude more Mediator complex proteins. In addition, super-enhancers preferentially associate with and activate genes key to cell state.

Enhancers function through co-operative and synergistic interactions between multiple transcription factors and coactivators (Carey, 1998; Carey et al., 1990; Giese et al., 1995; Kim and Maniatis, 1997; Thanos and Maniatis, 1995). Cooperative binding and synergistic activation confer increased sensitivity, so that small changes in activator concentration can lead to dramatic changes in activator binding and transcription of associated genes (Carey, 1998). This led us to hypothesize that highly sensitive super-enhancers driving key oncogenic drivers in multiple myeloma may account for the selective effect of BRD4 inhibition.

In this study, we show that BRD4 inhibition has a highly selective effect on critical tumor genes associated with super-enhancers. As expected, given its role as a general regulator of transcriptional pause release and its association with the Mediator complex, we found that BRD4 was located at a majority of active enhancers and promoters in tumor cells. Strikingly, extreme levels of BRD4 were found at a small subset of enhancer regions, which we have termed super-enhancers. These regions are similar to the super-enhancers described in mouse embryonic stem cells as discussed in Example 1 above. We found that binding of BRD4 and Mediator at super-enhancers was hyper-sensitive to loss of BRD4 binding through BET inhibition. This in turn corresponded to a dramatic loss of transcription at super-enhancer associated genes, such as MYC. Our data suggest a model of how inhibitors of generally acting chromatin regulators can exert a gene-specific effect, through the disruption of heavily occupied, cooperatively bound sites functioning at highly expressed tumor regulators. This concept may improve our understanding of how these drugs should be selected for the treatment of genetically-defined cancers.

Results Mediator and BRD4 Co-Occupy Promoters of Active Genes in Multiple Myeloma

In Example 1 above it was shown that Mediator and BRD4 co-occupy enhancers and active transcription start sites in embryonic stem cells and in differentiated cells. To determine whether Mediator and BRD4 co-occupy these sites in multiple myeloma cells, we used chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq) with antibodies directed against Mediator, Brd4 and various marks of enhancers and active transcription start sites in MM.1S cells (FIG. 6). The results, whether viewed by individual genes tracks or by meta-gene analysis, show that Mediator and BRD4 generally co-occupy enhancers and active transcription start sites (FIG. 6A, B). Signals for Mediator and BRD4 were found together with those for nucleosomes with the histone modification H3K27Ac in 8,000 regions lacking transcription start sites, and these were considered enhancers. Signals for BRD4 and Mediator were also found together with those for the histone modification H3K4me3 and RNA polymerase II at 14,000 annotated transcription start sites, and these were considered active transcription start sites. The levels of Mediator and BRD4 occupancy correlated with one another at both enhancers and transcription start sites (FIG. 6C), and the levels of BRD4 were correlated with the levels of RNA polymerase II at genes (FIG. 6D), consistent with the results observed in non-tumor cells in Example 1 above. These results indicate that Mediator and BRD4 generally co-occupy enhancers and active transcription start sites throughout the genome of MM.1S cells.

Super-Enhancers are Associated with Key Multiple Myeloma Genes

The sizes of enhancers identified by Mediator occupancy showed an unusual distribution, with a small subset of enhancers containing exceptional levels of Mediator protein (FIG. 7A). These 210 “super-enhancers” have features similar to those described in Example 1 above for mESCs (FIG. 7A). These are regions occupied, on average, by 16-fold more Mediator compared to normal enhancer regions. Super-enhancers also occupy larger genomic regions than normal enhancers, with a median size of 20 kb, 16-fold greater than the normal enhancer size of 1.3 kb. In addition to high Mediator occupancy, these enhancers were also bound by exceptional levels of BRD4, on average, 16-fold higher than normal enhancers (FIG. 7B).

As noted in Example 1 above, in ESCs and in differentiated cells, super-enhancers have exceptional transcription activation activity and are associated with highly expressed cell-type-specific genes that are located nearby. In MM.1S cells, super-enhancers were associated with highly expressed, cell-type specific genes, including genes known to be important in multiple myeloma (FIG. 7C). For example, the MM.1S MYC locus contains a chromosomal rearrangement that places MYC under the control of the IgH enhancers, which are highly active in the antibody producing plasma cells from which MM derives. The IgH-MYC locus contains a large, 40 kb super-enhancer, occupied by high levels of both BRD4 and MED1 (FIG. 7D). Super-enhancers were also found associated with the IRF4 gene (FIG. 7D), which encodes a key plasma cell transcription factor frequently deregulated in MM (Shaffer et al., 2008).

BRD4 occupancy at super-enhancers is highly sensitive to bromodomain inhibition

Enhancers are formed through co-operative and synergistic binding of multiple transcription factors and coactivators (Carey, 1998; Carey et al., 1990; Giese et al., 1995; Kim and Maniatis, 1997; Thanos and Maniatis, 1995). As a consequence of this binding behavior, enhancers bound by many cooperatively-interacting factors lose activity more rapidly than enhancers bound by fewer factors when the levels of enhancer-bound factors are reduced (Giniger and Ptashne, 1988; Griggs and Johnston, 1991). The presence of super-enhancers at MYC and other key genes associated with multiple myeloma led us to consider the hypothesis that super-enhancers are more sensitive to reduced levels of BRD4 than average enhancers. If super-enhancers are more sensitive to reduced levels of BRD4 than average enhancers, then super-enhancers should experience greater loss of BRD4 than average enhancers, and genes associated with super-enhancers might then experience a greater reduction of transcription than genes with average enhancers.

To test this hypothesis, we first examined the effects of various concentrations of JQ1 on genome-wide on BRD4 occupancy (FIG. 8A). During the course of the 6 hour treatments, JQ1 had little effect on MM1.S cell viability, as measured by ATP levels, while at later time points, JQ1 had a dramatic antiproliferative effect (FIG. 8B). As expected, MYC protein levels were significantly depleted by JQ1 treatment (FIG. 8C)(Delmore et al., 2011). In contrast, JQ1 did not affect BRD4 protein levels within cells, and did not significantly reduce ChIP efficiency (FIG. 8D). However, super-enhancers showed a greater loss of BRD4 occupancy when compared to regions with average or low amounts of BRD4 (FIG. 8E). The IgH enhancer was among those super-enhancers that showed significantly greater loss of BRD4 than typical enhancer regions with lower BRD4 occupancy, such as CD28 (FIG. 8G).

Loss of P-TEFb Accompanies BRD4 Inhibition

BRD4 recruits the active form of the positive transcription elongation factor P-TEFb, which stimulates pause release and transcription elongation (Bisgrove et al., 2007; Hargreaves et al., 2009; Jang et al., 2005; Jiang et al., 1998; Wu and Chiang, 2007; Wu et al., 2003; Yang et al., 2005). We used ChIP-Seq to investigate the global occupancy of P-TEFb in MM.1S cells and found that it generally occupies sites bound by Mediator and BRD4 (FIG. 9A). We next investigated whether the loss of BRD4 observed with JQ1 treatment is accompanied by loss of P-TEFb at enhancers and transcription start sites. JQ1 treatment did indeed reduce the levels of P-TEFb at sites where there was a reduction in BRD4 (FIG. 9B). Furthermore, P-TEFb was disproportionately lost at super-enhancers when compared to normal enhancers (FIG. 9C). We conclude that BET bromodomain inhibition of BRD4 leads to loss of P-TEFb at enhancers and transcription start sites, and that the inhibition has more profound effects at super-enhancers than at average enhancers.

To determine whether the loss of P-TEFb results in an elongation defect, we performed ChIP-seq of RNA Polymerase II (Pol II) after JQ1 treatment. We found that JQ1 treatment led to a global defect in transcriptional elongation, characterized by a loss of PolII in the gene body and 3′ transcription termination regions (FIG. 10). Further inspection of gene tracks revealed that key super-enhancer associated genes, including MYC, showed a dramatic defect in elongation (FIG. 10B). Globally, super-enhancer associated genes, had larger elongation defects in response to JQ1 than genes associated with normal enhancers (FIG. 10C) These results are consistent with the interpretation that genes driven by super-enhancers show more dramatic transcriptional defects due to reduced pause release and elongation of their transcripts.

Discussion

At present, inhibitors of chromatin regulators are gaining increased interest as potential therapeutic agents for treating cancer. Many chromatin regulators are understood to play general roles in the control of transcription, yet to reach significant clinical efficacy, small molecule inhibitors must have a selective effect on tumor cells. Several recent studies have shown that inhibition of the bromodomain protein BRD4 can indeed have a highly specific effect, causing the down regulation of key tumor drivers in several cancer types. In multiple myeloma, acute myeloid leukemia, and Burkitt's lymphoma, treatment with BET inhibitors led to a dramatic loss of MYC expression (Dawson et al., 2011; Delmore et al., 2011; Mertz et al., 2011; Zuber et al., 2011). Understanding how inhibitors of generally acting chromatin regulators can exert a selective effect will vastly improve our understanding of how these drugs should be selected for the treatment of genetically-defined cancers.

We have gained insight into this concept through our study of super-enhancers. We have found that, across many cell types, key regulators of cell state are associated with large, 10-40 kb enhancer domains, characterized by disproportionately high levels of MED1 binding and, as we have profiled in multiple myeloma, BRD4. Although these super-enhancers make up only a small percentage of the total number of enhancer regions, they account for a large fraction of total MED1 and BRD4 binding across the genome. Most significantly, we have found that super-enhancers are more sensitive to perturbation than typical enhancer regions.

We found that inhibition of BRD4 led to the dramatic loss of BRD4 and CDK9 binding at super-enhancers. In multiple myeloma, super-enhancers were associated with key oncogenic drivers, such as MYC. Disruption of super-enhancers by BRD4 inhibition led to a dramatic loss of expression of these critical tumor genes, accompanied by a potent antiproliferative effect.

Our results demonstrate that super-enhancers occupied by BRD4 regulate critical oncogenic drivers multiple myeloma and show that BRD4 inhibition leads to preferential disruption of these super-enhancers. This insight into the mechanism by which Brd4 inhibition causes selective loss of oncogene expression in these highly malignant blood cancers may have implications for future drug development in oncology. Many oncogenes critical to tumor cell function are highly expressed and may therefore be driven by super-enhancers. If so, preferential disruption of super-enhancer function may be a general approach to selectively inhibiting the oncogenic drivers of many tumor cells.

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TABLE 1 Super-enhancers from ESC. Based on NCBI Build 37 REGION_ID CHROM START STOP INT_STITCHED_45 chr1 13049615 13094765 INT_STITCHED_88 chr1 34130107 34134640 INT_STITCHED_100 chr1 36070190 36074608 INT_STITCHED_101 chr1 36111164 36118698 INT_STITCHED_108 chr1 37039139 37045411 INT_STITCHED_230 chr1 72260528 72261272 INT_STITCHED_237 chr1 72839563 72858199 INT_STITCHED_282 chr1 84857219 84887132 INT_STITCHED_315 chr1 91766947 91773527 INT_STITCHED_368 chr1 120538712 120545414 INT_STITCHED_372 chr1 120971968 120973737 INT_STITCHED_374 chr1 121201424 121202481 INT_STITCHED_376 chr1 121295085 121296031 INT_STITCHED_449 chr1 137071028 137096284 INT_STITCHED_464 chr1 138586629 138593131 INT_STITCHED_466 chr1 138841643 138850970 INT_STITCHED_508 chr1 154939892 154943709 INT_STITCHED_556 chr1 168054897 168073079 INT_STITCHED_559 chr1 169201106 169220423 INT_STITCHED_610 chr1 182818684 182819554 INT_STITCHED_611 chr1 182854521 182864307 INT_STITCHED_615 chr1 183948212 183961841 INT_STITCHED_746 chr2 20574602 20591747 INT_STITCHED_803 chr2 30913257 30925299 INT_STITCHED_812 chr2 32008891 32030736 INT_STITCHED_817 chr2 33282029 33300860 INT_STITCHED_928 chr2 71488013 71494617 INT_STITCHED_931 chr2 71575856 71583914 INT_STITCHED_1196 chr2 152002668 152003777 INT_STITCHED_1198 chr2 152552277 152563676 INT_STITCHED_1210 chr2 154242651 154254374 INT_STITCHED_1256 chr2 162856904 162860933 INT_STITCHED_1257 chr2 162877048 162893236 INT_STITCHED_1279 chr2 165981373 165983444 INT_STITCHED_1300 chr2 168589688 168617170 INT_STITCHED_1392 chr3 9641461 9655131 INT_STITCHED_1480 chr3 34544904 34553511 INT_STITCHED_1482 chr3 34633687 34660705 INT_STITCHED_1607 chr3 88375442 88380083 INT_STITCHED_1626 chr3 95455034 95468269 INT_STITCHED_1629 chr3 96380383 96382115 INT_STITCHED_1630 chr3 96479158 96484864 INT_STITCHED_1658 chr3 103008304 103019058 INT_STITCHED_1732 chr3 129247012 129261362 INT_STITCHED_1744 chr3 133181431 133197648 INT_STITCHED_1749 chr3 135208956 135210744 INT_STITCHED_1973 chr4 55469259 55491081 INT_STITCHED_2076 chr4 98507649 98514709 INT_STITCHED_2152 chr4 118743867 118745786 INT_STITCHED_2175 chr4 123300547 123303179 INT_STITCHED_2192 chr4 125211671 125223450 INT_STITCHED_2205 chr4 126875757 126879027 INT_STITCHED_2223 chr4 130178808 130180168 INT_STITCHED_2224 chr4 130195646 130196547 INT_STITCHED_2265 chr4 137148873 137153839 INT_STITCHED_2268 chr4 137329436 137357766 INT_STITCHED_2273 chr4 138000554 138006368 INT_STITCHED_2291 chr4 140826072 140840922 INT_STITCHED_2292 chr4 141120768 141126477 INT_STITCHED_2295 chr4 141616653 141627603 INT_STITCHED_2297 chr4 141721916 141726166 INT_STITCHED_2317 chr4 147459254 147463850 INT_STITCHED_2354 chr4 154537213 154538078 INT_STITCHED_2355 chr4 154563584 154564383 INT_STITCHED_2465 chr5 33873714 33880481 INT_STITCHED_2510 chr5 53933177 53947327 INT_STITCHED_2535 chr5 65255735 65256794 INT_STITCHED_2712 chr5 113758941 113775389 INT_STITCHED_2736 chr5 116845764 116860853 INT_STITCHED_2745 chr5 118884660 118896412 INT_STITCHED_2746 chr5 118951444 118960269 INT_STITCHED_2752 chr5 120029649 120037063 INT_STITCHED_2754 chr5 120129592 120171482 INT_STITCHED_2770 chr5 123584659 123590728 INT_STITCHED_2830 chr5 135417523 135421698 INT_STITCHED_3005 chr6 31834643 31852445 INT_STITCHED_3044 chr6 39370384 39371286 INT_STITCHED_3045 chr6 39395571 39396779 INT_STITCHED_3120 chr6 64961359 64985161 INT_STITCHED_3130 chr6 67061148 67064202 INT_STITCHED_3184 chr6 83839914 83844315 INT_STITCHED_3217 chr6 91640161 91661247 INT_STITCHED_3342 chr6 122290093 122293017 INT_STITCHED_3347 chr6 122612514 122614260 INT_STITCHED_3348 chr6 122640118 122657871 INT_STITCHED_3349 chr6 122714316 122720862 INT_STITCHED_3360 chr6 125383335 125398024 INT_STITCHED_3429 chr6 142458188 142461905 INT_STITCHED_3437 chr6 143047309 143065758 INT_STITCHED_3450 chr6 145223385 145225674 INT_STITCHED_3467 chr7 3193004 3218183 INT_STITCHED_3475 chr7 4772296 4777612 INT_STITCHED_3481 chr7 13599334 13600325 INT_STITCHED_3523 chr7 30982397 30983339 INT_STITCHED_3525 chr7 31248315 31250619 INT_STITCHED_3550 chr7 38812914 38816123 INT_STITCHED_3568 chr7 52806853 52814768 INT_STITCHED_3576 chr7 56592909 56604632 INT_STITCHED_3601 chr7 71092246 71102481 INT_STITCHED_3652 chr7 86355826 86368339 INT_STITCHED_3658 chr7 87159908 87169963 INT_STITCHED_3661 chr7 87274999 87276022 INT_STITCHED_3662 chr7 87333420 87345334 INT_STITCHED_3685 chr7 91027196 91051830 INT_STITCHED_3765 chr7 119831735 119835688 INT_STITCHED_3856 chr7 140304156 140307245 INT_STITCHED_3890 chr7 147131117 147136231 INT_STITCHED_3914 chr7 152036872 152050716 INT_STITCHED_3947 chr8 12499468 12504771 INT_STITCHED_4014 chr8 35023426 35027483 INT_STITCHED_4033 chr8 37602064 37613850 INT_STITCHED_4034 chr8 37642521 37671979 INT_STITCHED_4046 chr8 44405736 44406755 INT_STITCHED_4116 chr8 74834685 74840663 INT_STITCHED_4163 chr8 87174072 87174643 INT_STITCHED_4167 chr8 87996475 87997654 INT_STITCHED_4179 chr8 91514813 91540176 INT_STITCHED_4190 chr8 93351924 93355292 INT_STITCHED_4546 chr9 56382386 56395769 INT_STITCHED_4555 chr9 58119837 58128504 INT_STITCHED_4657 chr9 78207143 78223442 INT_STITCHED_4748 chr9 110849422 110863371 INT_STITCHED_4766 chr9 114458126 114474355 INT_STITCHED_4797 chr9 120585871 120600072 INT_STITCHED_4802 chr9 121244501 121254102 INT_STITCHED_4885 chr10 20802131 20830236 INT_STITCHED_4891 chr10 21546502 21549691 INT_STITCHED_4893 chr10 21700576 21708946 INT_STITCHED_4954 chr10 39977900 39978752 INT_STITCHED_4981 chr10 44110139 44112766 INT_STITCHED_5021 chr10 59420365 59437537 INT_STITCHED_5044 chr10 62346394 62361563 INT_STITCHED_5054 chr10 66380351 66383761 INT_STITCHED_5059 chr10 66546199 66564235 INT_STITCHED_5091 chr10 75335464 75345568 INT_STITCHED_5092 chr10 75400370 75401358 INT_STITCHED_5100 chr10 76655655 76662360 INT_STITCHED_5111 chr10 79508474 79515168 INT_STITCHED_5140 chr10 85002060 85006553 INT_STITCHED_5325 chr11 8466451 8486876 INT_STITCHED_5331 chr11 9015537 9017663 INT_STITCHED_5340 chr11 12357626 12370205 INT_STITCHED_5427 chr11 33427175 33451476 INT_STITCHED_5484 chr11 52173182 52184686 INT_STITCHED_5499 chr11 54767341 54785832 INT_STITCHED_5533 chr11 62324296 62327251 INT_STITCHED_5553 chr11 66733372 66746990 INT_STITCHED_5555 chr11 66824791 66838230 INT_STITCHED_5565 chr11 69517060 69522803 INT_STITCHED_5597 chr11 77697704 77718786 INT_STITCHED_5666 chr11 88481360 88491812 INT_STITCHED_5711 chr11 97517673 97524159 INT_STITCHED_5719 chr11 98823511 98826466 INT_STITCHED_5741 chr11 102190649 102193692 INT_STITCHED_5752 chr11 104150171 104167544 INT_STITCHED_5768 chr11 107296669 107310982 INT_STITCHED_5819 chr11 116943025 116953583 INT_STITCHED_5831 chr11 117833701 117838253 INT_STITCHED_5875 chr12 12790432 12795881 INT_STITCHED_5876 chr12 12810177 12811020 INT_STITCHED_5880 chr12 12933791 12950936 INT_STITCHED_5995 chr12 55407498 55415046 INT_STITCHED_6000 chr12 56587347 56607146 INT_STITCHED_6004 chr12 57385208 57400114 INT_STITCHED_6112 chr12 87807046 87820319 INT_STITCHED_6113 chr12 87839385 87846192 INT_STITCHED_6118 chr12 88239069 88245155 INT_STITCHED_6151 chr12 103940487 103953004 INT_STITCHED_6186 chr12 111655417 111656705 INT_STITCHED_6187 chr12 111709296 111710794 INT_STITCHED_6188 chr12 111725920 111743677 INT_STITCHED_6460 chr13 64069823 64082322 INT_STITCHED_6544 chr13 96295094 96306119 INT_STITCHED_6557 chr13 98052562 98062842 INT_STITCHED_6559 chr13 98202400 98225162 INT_STITCHED_6615 chr13 110418702 110442750 INT_STITCHED_6709 chr14 22293688 22308989 INT_STITCHED_6789 chr14 49273113 49283200 INT_STITCHED_6815 chr14 55704349 55705463 INT_STITCHED_6859 chr14 64118817 64131901 INT_STITCHED_6864 chr14 65251303 65269514 INT_STITCHED_6887 chr14 71022659 71035930 INT_STITCHED_6904 chr14 76894682 76915946 INT_STITCHED_6906 chr14 77015215 77030315 INT_STITCHED_6957 chr14 99738540 99755307 INT_STITCHED_6981 chr14 106250319 106260753 INT_STITCHED_6982 chr14 106296486 106304433 INT_STITCHED_7104 chr15 25654102 25704265 INT_STITCHED_7202 chr15 61918415 61924748 INT_STITCHED_7248 chr15 77168852 77187251 INT_STITCHED_7285 chr15 88539016 88539831 INT_STITCHED_7317 chr15 97198605 97227633 INT_STITCHED_7318 chr15 97422878 97425328 INT_STITCHED_7343 chr15 103349226 103353500 INT_STITCHED_7359 chr16 8758173 8779472 INT_STITCHED_7434 chr16 23099373 23103471 INT_STITCHED_7452 chr16 29657509 29668114 INT_STITCHED_7597 chr16 84769173 84780686 INT_STITCHED_7680 chr17 10549089 10570838 INT_STITCHED_7728 chr17 26631721 26648689 INT_STITCHED_7747 chr17 29209618 29218426 INT_STITCHED_7752 chr17 29587776 29588942 INT_STITCHED_7767 chr17 31939569 31956756 INT_STITCHED_7784 chr17 35639211 35642435 INT_STITCHED_7792 chr17 37110202 37134996 INT_STITCHED_7794 chr17 37209046 37217726 INT_STITCHED_7812 chr17 45593477 45596503 INT_STITCHED_7822 chr17 47640414 47649043 INT_STITCHED_7876 chr17 66818723 66836409 INT_STITCHED_7884 chr17 71096763 71100905 INT_STITCHED_7886 chr17 71177302 71179956 INT_STITCHED_7887 chr17 71213804 71222433 INT_STITCHED_7888 chr17 71241991 71250610 INT_STITCHED_8114 chr18 35202713 35203454 INT_STITCHED_8124 chr18 36412873 36414154 INT_STITCHED_8136 chr18 38538325 38551037 INT_STITCHED_8139 chr18 38760823 38761958 INT_STITCHED_8140 chr18 38788269 38796942 INT_STITCHED_8148 chr18 40467587 40468140 INT_STITCHED_8209 chr18 61787544 61788400 INT_STITCHED_8260 chr18 75504155 75505202 INT_STITCHED_8261 chr18 75520332 75527277 INT_STITCHED_8264 chr18 75738693 75745073 INT_STITCHED_8324 chr19 5835881 5847014 INT_STITCHED_8378 chr19 21858770 21866770 INT_STITCHED_8385 chr19 23139991 23170189 INT_STITCHED_8386 chr19 23207455 23208806 INT_STITCHED_8399 chr19 25553498 25564092 INT_STITCHED_8519 chr19 53523440 53535319 INT_STITCHED_8554 chrX 7578969 7597907 INT_STITCHED_8629 chrX 50098631 50114110

TABLE 2 Multiple Myeloma Super-enhancers. Based on Gene Build hg 18 REGION_ID CHROM START STOP 3_MM1S_MED1_DMSO_2_11472_lociStitched chr22 21597907 21632017 12_MM1S_MED1_DMSO_2_12661_lociStitched chr3 142561889 142658635 5_MM1S_MED1_DMSO_2_11467_lociStitched chr22 21520124 21576243 3_MM1S_MED1_DMSO_2_15142_lociStitched chr6 7822980 7864682 27_MM1S_MED1_DMSO_2_15896_lociStitched chr6 108969554 109119470 10_MM1S_MED1_DMSO_2_883_lociStitched chr1 117943520 118031299 13_MM1S_MED1_DMSO_2_9297_lociStitched chr2 37383079 37478117 7_MM1S_MED1_DMSO_2_1421_lociStitched chr1 201502736 201564474 6_MM1S_MED1_DMSO_2_10778_lociStitched chr20 29712568 29775967 4_MM1S_MED1_DMSO_2_3066_lociStitched chr11 64939923 64979931 12_MM1S_MED1_DMSO_2_10818_lociStitched chr20 31862228 31936793 15_MM1S_MED1_DMSO_2_19349_lociStitched chrX 130689710 130790383 6_MM1S_MED1_DMSO_2_15061_lociStitched chr6 235131 282880 MM1S_MED1_DMSO_2_4011 chr12 51868026 51890008 13_MM1S_MED1_DMSO_2_6359_lociStitched chr16 11662193 11750399 5_MM1S_MED1_DMSO_2_19070_lociStitched chrX 48652795 48690448 9_MM1S_MED1_DMSO_2_13894_lociStitched chr4 185522607 185586220 2_MM1S_MED1_DMSO_2_15298_lociStitched chr6 26263259 26281958 4_MM1S_MED1_DMSO_2_2709_lociStitched chr11 10280174 10301780 7_MM1S_MED1_DMSO_2_11528_lociStitched chr22 27516134 27555928 5_MM1S_MED1_DMSO_2_7255_lociStitched chr17 29712450 29745538 9_MM1S_MED1_DMSO_2_9712_lociStitched chr2 98426920 98498831 10_MM1S_MED1_DMSO_2_5371_lociStitched chr14 90884807 90955651 3_MM1S_MED1_DMSO_2_7984_lociStitched chr18 9050438 9074417 8_MM1S_MED1_DMSO_2_16690_lociStitched chr7 55566748 55610180 1_MM1S_MED1_DMSO_2_935_lociStitched chr1 148122391 148127826 3_MM1S_MED1_DMSO_2_3735_lociStitched chr12 12748016 12781726 4_MM1S_MED1_DMSO_2_2546_lociStitched chr10 125812311 125857688 2_MM1S_MED1_DMSO_2_1862_lociStitched chr10 11242759 11275331 3_MM1S_MED1_DMSO_2_929_lociStitched chr1 147470833 147491868 MM1S_MED1_DMSO_2_15293 chr6 26161696 26165891 3_MM1S_MED1_DMSO_2_9167_lociStitched chr2 20254183 20289776 1_MM1S_MED1_DMSO_2_15301_lociStitched chr6 26303073 26309499 11_MM1S_MED1_DMSO_2_17447_lociStitched chr8 27264787 27340169 3_MM1S_MED1_DMSO_2_178_lociStitched chr1 17094196 17113973 13_MM1S_MED1_DMSO_2_17882_lociStitched chr8 120985081 121017049 3_MM1S_MED1_DMSO_2_1025_lociStitched chr1 153174936 153197206 1_MM1S_MED1_DMSO_2_13984_lociStitched chr5 1364911 1374105 MM1S_MED1_DMSO_2_15361 chr6 27964884 27972054 3_MM1S_MED1_DMSO_2_3071_lociStitched chr11 65020047 65035435 5_MM1S_MED1_DMSO_2_18418_lociStitched chr9 92710817 92746187 3_MM1S_MED1_DMSO_2_13885_lociStitched chr4 185421650 185447815 5_MM1S_MED1_DMSO_2_9691_lociStitched chr2 96554603 96584612 10_MM1S_MED1_DMSO_2_15652_lociStitched chr6 52501063 52557406 MM1S_MED1_DMSO_2_7572 chr17 53760011 53773039 6_MM1S_MED1_DMSO_2_15868_lociStitched chr6 106637997 106665835 1_MM1S_MED1_DMSO_2_15308_lociStitched chr6 26377785 26382951 2_MM1S_MED1_DMSO_2_7420_lociStitched chr17 38792419 38802756 9_MM1S_MED1_DMSO_2_14628_lociStitched chr5 131818986 131870127 3_MM1S_MED1_DMSO_2_13539_lociStitched chr4 90429430 90459112 4_MM1S_MED1_DMSO_2_12859_lociStitched chr3 178538717 178562722 4_MM1S_MED1_DMSO_2_4371_lociStitched chr12 107533824 107560420 4_MM1S_MED1_DMSO_2_15314_lociStitched chr6 26449533 26475951 MM1S_MED1_DMSO_2_15291 chr6 26138365 26142878 1_MM1S_MED1_DMSO_2_15296_lociStitched chr6 26230241 26235063 9_MM1S_MED1_DMSO_2_5477_lociStitched chr14 105096168 105120688 2_MM1S_MED1_DMSO_2_12120_lociStitched chr3 46220865 46232443 MM1S_MED1_DMSO_2_15292 chr6 26150596 26154952 2_MM1S_MED1_DMSO_2_5546_lociStitched chr15 29333964 29348240 1_MM1S_MED1_DMSO_2_176_lociStitched chr1 16712194 16713944 1_MM1S_MED1_DMSO_2_12853_lociStitched chr3 178395376 178403353 1_MM1S_MED1_DMSO_2_10897_lociStitched chr20 36931952 36938862 2_MM1S_MED1_DMSO_2_9810_lociStitched chr2 112172513 112182538 5_MM1S_MED1_DMSO_2_497_lociStitched chr1 44945879 44970311 7_MM1S_MED1_DMSO_2_8152_lociStitched chr18 44693277 44734029 1_MM1S_MED1_DMSO_2_3010_lociStitched chr11 62362909 62367338 2_MM1S_MED1_DMSO_2_1718_lociStitched chr1 232800286 232816291 7_MM1S_MED1_DMSO_2_16140_lociStitched chr6 138287960 138339719 4_MM1S_MED1_DMSO_2_16924_lociStitched chr7 101851129 101879762 7_MM1S_MED1_DMSO_2_3539_lociStitched chr11 128090989 128134946 5_MM1S_MED1_DMSO_2_13905_lociStitched chr4 185603808 185634087 5_MM1S_MED1_DMSO_2_8400_lociStitched chr19 2546568 2579792 4_MM1S_MED1_DMSO_2_17232_lociStitched chr7 149685067 149715545 9_MM1S_MED1_DMSO_2_6090_lociStitched chr15 88364067 88447544 7_MM1S_MED1_DMSO_2_5551_lociStitched chr15 29404247 29447806 6_MM1S_MED1_DMSO_2_908_lociStitched chr1 144138338 144169442 6_MM1S_MED1_DMSO_2_2813_lociStitched chr11 22633909 22661308 2_MM1S_MED1_DMSO_2_11309_lociStitched chr21 40247390 40265606 3_MM1S_MED1_DMSO_2_11459_lociStitched chr22 21406975 21431657 4_MM1S_MED1_DMSO_2_4023_lociStitched chr12 52133823 52163301 3_MM1S_MED1_DMSO_2_6783_lociStitched chr16 78185190 78197918 2_MM1S_MED1_DMSO_2_2451_lociStitched chr10 112094075 112109393 4_MM1S_MED1_DMSO_2_3671_lociStitched chr12 6916226 6942174 3_MM1S_MED1_DMSO_2_11367_lociStitched chr21 44381407 44405755 6_MM1S_MED1_DMSO_2_18632_lociStitched chr9 122670221 122707139 5_MM1S_MED1_DMSO_2_7098_lociStitched chr17 16810645 16836243 5_MM1S_MED1_DMSO_2_12822_lociStitched chr3 173284485 173309559 3_MM1S_MED1_DMSO_2_7795_lociStitched chr17 72647302 72672300 5_MM1S_MED1_DMSO_2_14194_lociStitched chr5 55473448 55500561 4_MM1S_MED1_DMSO_2_5843_lociStitched chr15 63374708 63385346 7_MM1S_MED1_DMSO_2_12921_lociStitched chr3 184711984 184757118 3_MM1S_MED1_DMSO_2_13004_lociStitched chr3 195330092 195342991 6_MM1S_MED1_DMSO_2_1869_lociStitched chr10 11323723 11353214 6_MM1S_MED1_DMSO_2_5884_lociStitched chr15 66355713 66386773 4_MM1S_MED1_DMSO_2_16493_lociStitched chr7 25953531 25975640 2_MM1S_MED1_DMSO_2_17945_lociStitched chr8 128815143 128831262 3_MM1S_MED1_DMSO_2_6443_lociStitched chr16 23241697 23269855 1_MM1S_MED1_DMSO_2_15307_lociStitched chr6 26356880 26361949 4_MM1S_MED1_DMSO_2_1007_lociStitched chr1 152636911 152660538 12_MM1S_MED1_DMSO_2_12617_lociStitched chr3 134643043 134708940 3_MM1S_MED1_DMSO_2_1629_lociStitched chr1 224363473 224383373 3_MM1S_MED1_DMSO_2_2794_lociStitched chr11 19406910 19422183 2_MM1S_MED1_DMSO_2_4947_lociStitched chr13 113545919 113557086 3_MM1S_MED1_DMSO_2_15146_lociStitched chr6 7903492 7922524 2_MM1S_MED1_DMSO_2_9355_lociStitched chr2 43297983 43310825 MM1S_MED1_DMSO_2_15353 chr6 27882353 27887636 1_MM1S_MED1_DMSO_2_117_lociStitched chr1 11889871 11893140 5_MM1S_MED1_DMSO_2_11097_lociStitched chr20 55481270 55509295 1_MM1S_MED1_DMSO_2_10440_lociStitched chr2 231437101 231447701 3_MM1S_MED1_DMSO_2_340_lociStitched chr1 30988720 31005936 7_MM1S_MED1_DMSO_2_15801_lociStitched chr6 90115755 90142733 3_MM1S_MED1_DMSO_2_9401_lociStitched chr2 47380900 47404415 1_MM1S_MED1_DMSO_2_15359_lociStitched chr6 27939690 27944056 6_MM1S_MED1_DMSO_2_16939_lociStitched chr7 104350354 104392312 4_MM1S_MED1_DMSO_2_14621_lociStitched chr5 131777514 131802069 9_MM1S_MED1_DMSO_2_7852_lociStitched chr17 74224147 74290965 5_MM1S_MED1_DMSO_2_10765_lociStitched chr20 25209731 25248761 3_MM1S_MED1_DMSO_2_11306_lociStitched chr21 40217819 40231333 1_MM1S_MED1_DMSO_2_4955_lociStitched chr13 113847326 113853279 9_MM1S_MED1_DMSO_2_17774_lociStitched chr8 96022708 96074048 1_MM1S_MED1_DMSO_2_15467_lociStitched chr6 33042969 33050991 2_MM1S_MED1_DMSO_2_10245_lociStitched chr2 201688028 201701230 2_MM1S_MED1_DMSO_2_3620_lociStitched chr12 4086510 4100254 1_MM1S_MED1_DMSO_2_11604_lociStitched chr22 35056163 35061482 5_MM1S_MED1_DMSO_2_8117_lociStitched chr18 40542132 40560323 5_MM1S_MED1_DMSO_2_17304_lociStitched chr8 2016787 2037760 11_MM1S_MED1_DMSO_2_7624_lociStitched chr17 59486930 59536700 5_MM1S_MED1_DMSO_2_7793_lociStitched chr17 72590686 72618288 2_MM1S_MED1_DMSO_2_15176_lociStitched chr6 11937666 11944210 3_MM1S_MED1_DMSO_2_8375_lociStitched chr19 2032758 2049163 5_MM1S_MED1_DMSO_2_10377_lociStitched chr2 219449340 219471887 1_MM1S_MED1_DMSO_2_18431_lociStitched chr9 92992632 92996907 MM1S_MED1_DMSO_2_8809 chr19 44583388 44595931 6_MM1S_MED1_DMSO_2_19132_lociStitched chrX 58141354 58176568 2_MM1S_MED1_DMSO_2_11329_lociStitched chr21 42353240 42371485 3_MM1S_MED1_DMSO_2_3939_lociStitched chr12 46487401 46506636 2_MM1S_MED1_DMSO_2_2457_lociStitched chr10 112205500 112215498 6_MM1S_MED1_DMSO_2_6074_lociStitched chr15 87434644 87475737 2_MM1S_MED1_DMSO_2_1061_lociStitched chr1 154382144 154399688 6_MM1S_MED1_DMSO_2_14486_lociStitched chr5 109279819 109314997 2_MM1S_MED1_DMSO_2_218_lociStitched chr1 23723110 23739682 6_MM1S_MED1_DMSO_2_11882_lociStitched chr3 5197581 5231167 5_MM1S_MED1_DMSO_2_8393_lociStitched chr19 2419984 2446976 1_MM1S_MED1_DMSO_2_11487_lociStitched chr22 22514623 22522474 5_MM1S_MED1_DMSO_2_11633_lociStitched chr22 35940694 35972007 4_MM1S_MED1_DMSO_2_13300_lociStitched chr4 39868398 39884094 2_MM1S_MED1_DMSO_2_15875_lociStitched chr6 106717009 106735272 4_MM1S_MED1_DMSO_2_16685_lociStitched chr7 55537132 55553461 2_MM1S_MED1_DMSO_2_13593_lociStitched chr4 105626955 105636498 1_MM1S_MED1_DMSO_2_5492_lociStitched chr14 105394828 105400642 2_MM1S_MED1_DMSO_2_1032_lociStitched chr1 153236845 153257390 6_MM1S_MED1_DMSO_2_6769_lociStitched chr16 77326423 77362760 4_MM1S_MED1_DMSO_2_15040_lociStitched chr5 180161278 180192831 2_MM1S_MED1_DMSO_2_11510_lociStitched chr22 25335621 25345570 4_MM1S_MED1_DMSO_2_5303_lociStitched chr14 76557983 76580142 3_MM1S_MED1_DMSO_2_15065_lociStitched chr6 334189 345497 2_MM1S_MED1_DMSO_2_10912_lociStitched chr20 40143996 40158547 5_MM1S_MED1_DMSO_2_6691_lociStitched chr16 66841952 66878349 1_MM1S_MED1_DMSO_2_7334_lociStitched chr17 35163138 35168797 2_MM1S_MED1_DMSO_2_18434_lociStitched chr9 93221024 93234776 3_MM1S_MED1_DMSO_2_8242_lociStitched chr18 58955785 58981327 1_MM1S_MED1_DMSO_2_13003_lociStitched chr3 195300012 195305617 2_MM1S_MED1_DMSO_2_6646_lociStitched chr16 65106878 65117734 3_MM1S_MED1_DMSO_2_4266_lociStitched chr12 93065052 93093164 3_MM1S_MED1_DMSO_2_11259_lociStitched chr21 35158227 35184979 4_MM1S_MED1_DMSO_2_3801_lociStitched chr12 26157584 26171339 2_MM1S_MED1_DMSO_2_16133_lociStitched chr6 138228659 138247051 3_MM1S_MED1_DMSO_2_17236_lociStitched chr7 149731864 149749863 4_MM1S_MED1_DMSO_2_13002_lociStitched chr3 195258091 195287025 2_MM1S_MED1_DMSO_2_953_lociStitched chr1 148798802 148808298 2_MM1S_MED1_DMSO_2_1450_lociStitched chr1 203508812 203524935 2_MM1S_MED1_DMSO_2_15283_lociStitched chr6 25511304 25522342 3_MM1S_MED1_DMSO_2_290_lociStitched chr1 26890818 26902191 5_MM1S_MED1_DMSO_2_7990_lociStitched chr18 9091649 9111559 7_MM1S_MED1_DMSO_2_18762_lociStitched chr9 133102585 133143969 1_MM1S_MED1_DMSO_2_11360_lociStitched chr21 44021842 44029128 2_MM1S_MED1_DMSO_2_3442_lociStitched chr11 118244109 118249498 3_MM1S_MED1_DMSO_2_240_lociStitched chr1 24384810 24406266 3_MM1S_MED1_DMSO_2_13402_lociStitched chr4 71744317 71766940 1_MM1S_MED1_DMSO_2_1504_lociStitched chr1 207342554 207349164 2_MM1S_MED1_DMSO_2_3411_lociStitched chr11 114631374 114641681 1_MM1S_MED1_DMSO_2_6445_lociStitched chr16 23321100 23326979 3_MM1S_MED1_DMSO_2_15550_lociStitched chr6 37230628 37252404 2_MM1S_MED1_DMSO_2_13986_lociStitched chr5 1388551 1399215 4_MM1S_MED1_DMSO_2_1441_lociStitched chr1 202729083 202757890 4_MM1S_MED1_DMSO_2_1469_lociStitched chr1 204784341 204809621 1_MM1S_MED1_DMSO_2_10460_lociStitched chr2 232278796 232285774 2_MM1S_MED1_DMSO_2_2970_lociStitched chr11 60354930 60369771 3_MM1S_MED1_DMSO_2_8650_lociStitched chr19 16555465 16572388 9_MM1S_MED1_DMSO_2_12125_lociStitched chr3 46292850 46331709 1_MM1S_MED1_DMSO_2_16944_lociStitched chr7 104438848 104443908 3_MM1S_MED1_DMSO_2_19007_lociStitched chrX 39838174 39854463 1_MM1S_MED1_DMSO_2_3626_lociStitched chr12 4247853 4257225 2_MM1S_MED1_DMSO_2_14483_lociStitched chr5 109219736 109229823 6_MM1S_MED1_DMSO_2_12115_lociStitched chr3 46081401 46126461 3_MM1S_MED1_DMSO_2_11151_lociStitched chr20 61828935 61842486 4_MM1S_MED1_DMSO_2_5613_lociStitched chr15 38175241 38196125 4_MM1S_MED1_DMSO_2_13278_lociStitched chr4 37983729 37998765 6_MM1S_MED1_DMSO_2_5325_lociStitched chr14 81000404 81025576 5_MM1S_MED1_DMSO_2_8632_lociStitched chr19 16112417 16131135 7_MM1S_MED1_DMSO_2_6134_lociStitched chr15 91147531 91189935 1_MM1S_MED1_DMSO_2_7450_lociStitched chr17 40653952 40663191 5_MM1S_MED1_DMSO_2_1463_lociStitched chr1 204455280 204477658 3_MM1S_MED1_DMSO_2_12583_lociStitched chr3 130511014 130530874 1_MM1S_MED1_DMSO_2_19115_lociStitched chrX 56805175 56811038 2_MM1S_MED1_DMSO_2_811_lociStitched chr1 110963171 110982799 1_MM1S_MED1_DMSO_2_7885_lociStitched chr17 77090061 77097539 3_MM1S_MED1_DMSO_2_11917_lociStitched chr3 13010123 13036559 5_MM1S_MED1_DMSO_2_2179_lociStitched chr10 73677336 73694126 3_MM1S_MED1_DMSO_2_8045_lociStitched chr18 19057373 19077707 1_MM1S_MED1_DMSO_2_14417_lociStitched chr5 90711139 90716188 2_MM1S_MED1_DMSO_2_4222_lociStitched chr12 88262387 88273597 1_MM1S_MED1_DMSO_2_1055_lociStitched chr1 154210608 154218896 4_MM1S_MED1_DMSO_2_13888_lociStitched chr4 185476602 185507051 5_MM1S_MED1_DMSO_2_13340_lociStitched chr4 47873764 47901113 3_MM1S_MED1_DMSO_2_902_lociStitched chr1 144093230 144111474 4_MM1S_MED1_DMSO_2_4375_lociStitched chr12 107581795 107622903 3_MM1S_MED1_DMSO_2_7801_lociStitched chr17 72740997 72755489 2_MM1S_MED1_DMSO_2_2458_lociStitched chr10 112245714 112254934 11_MM1S_MED1_DMSO_2_14962_lociStitched chr5 173243900 173289403 4_MM1S_MED1_DMSO_2_12387_lociStitched chr3 99962343 99978843 1_MM1S_MED1_DMSO_2_4479_lociStitched chr12 119212631 119215958 3_MM1S_MED1_DMSO_2_15872_lociStitched chr6 106692441 106702198 2_MM1S_MED1_DMSO_2_4368_lociStitched chr12 107478295 107494548 3_MM1S_MED1_DMSO_2_8359_lociStitched chr19 1598817 1620929 5_MM1S_MED1_DMSO_2_11087_lociStitched chr20 55390112 55408865 5_MM1S_MED1_DMSO_2_3367_lociStitched chr11 110737473 110765459 1_MM1S_MED1_DMSO_2_17494_lociStitched chr8 29685550 29690431 5_MM1S_MED1_DMSO_2_9346_lociStitched chr2 42179512 42210718 9_MM1S_MED1_DMSO_2_12137_lociStitched chr3 46384095 46413568 4_MM1S_MED1_DMSO_2_2241_lociStitched chr10 80670951 80690429 3_MM1S_MED1_DMSO_2_18151_lociStitched chr9 9596419 9605712 4_MM1S_MED1_DMSO_2_5951_lociStitched chr15 72850107 72865537 6_MM1S_MED1_DMSO_2_9773_lociStitched chr2 109176497 109219823 2_MM1S_MED1_DMSO_2_11509_lociStitched chr22 25312119 25321438 2_MM1S_MED1_DMSO_2_13009_lociStitched chr3 195504620 195516950 4_MM1S_MED1_DMSO_2_11609_lociStitched chr22 35102731 35115007 7_MM1S_MED1_DMSO_2_5487_lociStitched chr14 105217337 105240489 1_MM1S_MED1_DMSO_2_10174_lociStitched chr2 192248312 192253669 3_MM1S_MED1_DMSO_2_7356_lociStitched chr17 35720293 35737137 4_MM1S_MED1_DMSO_2_1849_lociStitched chr10 7553027 7575263 4_MM1S_MED1_DMSO_2_16642_lociStitched chr7 47479754 47504874 3_MM1S_MED1_DMSO_2_14100_lociStitched chr5 32607763 32625969 5_MM1S_MED1_DMSO_2_4572_lociStitched chr12 123957232 123991926 4_MM1S_MED1_DMSO_2_2466_lociStitched chr10 112590984 112617972 1_MM1S_MED1_DMSO_2_11372_lociStitched chr21 44484038 44489285 8_MM1S_MED1_DMSO_2_8848_lociStitched chr19 46720121 46762201 2_MM1S_MED1_DMSO_2_2455_lociStitched chr10 112162427 112174574 3_MM1S_MED1_DMSO_2_6671_lociStitched chr16 66137623 66158813 3_MM1S_MED1_DMSO_2_19339_lociStitched chrX 130662431 130673564 2_MM1S_MED1_DMSO_2_1640_lociStitched chr1 224906864 224919127 3_MM1S_MED1_DMSO_2_7431_lociStitched chr17 39630911 39655723 1_MM1S_MED1_DMSO_2_8114_lociStitched chr18 40512420 40517489 1_MM1S_MED1_DMSO_2_14692_lociStitched chr5 138749622 138758419 3_MM1S_MED1_DMSO_2_1123_lociStitched chr1 158943494 158980488 4_MM1S_MED1_DMSO_2_16250_lociStitched chr6 157897104 157913718 2_MM1S_MED1_DMSO_2_17101_lociStitched chr7 130440752 130460529 3_MM1S_MED1_DMSO_2_9135_lociStitched chr2 11801032 11812720 3_MM1S_MED1_DMSO_2_10929_lociStitched chr20 42002450 42018666 3_MM1S_MED1_DMSO_2_1119_lociStitched chr1 158908226 158921742 1_MM1S_MED1_DMSO_2_3090_lociStitched chr11 65380453 65385752 2_MM1S_MED1_DMSO_2_16369_lociStitched chr7 5531468 5539806 5_MM1S_MED1_DMSO_2_13495_lociStitched chr4 84352012 84381789 2_MM1S_MED1_DMSO_2_17959_lociStitched chr8 129734648 129741973 1_MM1S_MED1_DMSO_2_5907_lociStitched chr15 68174162 68181768 4_MM1S_MED1_DMSO_2_10987_lociStitched chr20 45820090 45849423 2_MM1S_MED1_DMSO_2_5964_lociStitched chr15 73121792 73127799 2_MM1S_MED1_DMSO_2_17479_lociStitched chr8 29253249 29266444 5_MM1S_MED1_DMSO_2_18891_lociStitched chrX 10025533 10050677 2_MM1S_MED1_DMSO_2_17880_lociStitched chr8 120954422 120969636 1_MM1S_MED1_DMSO_2_1813_lociStitched chr10 3814293 3818876 5_MM1S_MED1_DMSO_2_9497_lociStitched chr2 64716540 64748251 4_MM1S_MED1_DMSO_2_7748_lociStitched chr17 71366025 71387309 6_MM1S_MED1_DMSO_2_2420_lociStitched chr10 105235066 105265831 3_MM1S_MED1_DMSO_2_7698_lociStitched chr17 68094083 68113162 2_MM1S_MED1_DMSO_2_18473_lociStitched chr9 97295762 97314118 1_MM1S_MED1_DMSO_2_7313_lociStitched chr17 34110323 34116969 7_MM1S_MED1_DMSO_2_4966_lociStitched chr13 114042783 114062417 3_MM1S_MED1_DMSO_2_14016_lociStitched chr5 6528481 6550072 1_MM1S_MED1_DMSO_2_10942_lociStitched chr20 42704197 42716062 4_MM1S_MED1_DMSO_2_13987_lociStitched chr5 1541550 1578016 3_MM1S_MED1_DMSO_2_13707_lociStitched chr4 129949673 129960374 2_MM1S_MED1_DMSO_2_10549_lociStitched chr2 238264326 238277907 4_MM1S_MED1_DMSO_2_19321_lociStitched chrX 128720479 128739812 3_MM1S_MED1_DMSO_2_9743_lociStitched chr2 105694868 105718268 1_MM1S_MED1_DMSO_2_9393_lociStitched chr2 47061614 47068522 3_MM1S_MED1_DMSO_2_10581_lociStitched chr2 241152963 241176172 5_MM1S_MED1_DMSO_2_2158_lociStitched chr10 71906942 71940173 3_MM1S_MED1_DMSO_2_3127_lociStitched chr11 66789831 66814109 2_MM1S_MED1_DMSO_2_12973_lociStitched chr3 188262377 188274985 1_MM1S_MED1_DMSO_2_14147_lociStitched chr5 43072552 43079610 5_MM1S_MED1_DMSO_2_7714_lociStitched chr17 70249246 70279117 2_MM1S_MED1_DMSO_2_13272_lociStitched chr4 37805684 37812390 1_MM1S_MED1_DMSO_2_9642_lociStitched chr2 86073843 86082122 1_MM1S_MED1_DMSO_2_13666_lociStitched chr4 121888607 121891728 2_MM1S_MED1_DMSO_2_6598_lociStitched chr16 55501343 55510262 4_MM1S_MED1_DMSO_2_12038_lociStitched chr3 39222524 39251963 2_MM1S_MED1_DMSO_2_1926_lociStitched chr10 15866384 15871377 2_MM1S_MED1_DMSO_2_5835_lociStitched chr15 62961116 62976322 2_MM1S_MED1_DMSO_2_11661_lociStitched chr22 37031196 37044926 1_MM1S_MED1_DMSO_2_2098_lociStitched chr10 63326304 63335210 4_MM1S_MED1_DMSO_2_3547_lociStitched chr11 128727439 128752307 3_MM1S_MED1_DMSO_2_12969_lociStitched chr3 188185946 188202148 2_MM1S_MED1_DMSO_2_11345_lociStitched chr21 43454397 43471457 3_MM1S_MED1_DMSO_2_19091_lociStitched chrX 52966103 52981642 3_MM1S_MED1_DMSO_2_8625_lociStitched chr19 16041917 16058919 3_MM1S_MED1_DMSO_2_1534_lociStitched chr1 209753487 209768728 3_MM1S_MED1_DMSO_2_2769_lociStitched chr11 16923726 16943228

TABLE 3 Glioblastoma Super-Enhancers. Based on Gene Build hg18 REGION_ID CHROM START STOP 18_U87_MED1_20020_lociStitched chr3 45100470 45243521 12_U87_MED1_7111_lociStitched chr12 64271490 64380497 22_U87_MED1_17388_lociStitched chr2 237744314 237896194 8_U87_MED1_7790_lociStitched chr12 126279637 126344656 16_U87_MED1_25966_lociStitched chr6 44066339 44153887 20_U87_MED1_17421_lociStitched chr2 237957090 238086756 13_U87_MED1_24508_lociStitched chr5 135356769 135440815 5_U87_MED1_21695_lociStitched chr3 195773224 195801953 10_U87_MED1_28029_lociStitched chr7 100523787 100571097 6_U87_MED1_32110_lociStitched chrX 45479800 45553892 U87_MED1_6148 chr11 121548066 121570391 19_U87_MED1_15336_lociStitched chr2 46879598 46970410 6_U87_MED1_28324_lociStitched chr7 130215723 130260073 17_U87_MED1_28910_lociStitched chr8 23203324 23280028 6_U87_MED1_18087_lociStitched chr20 45376522 45424087 4_U87_MED1_5653_lociStitched chr11 64940094 64979948 9_U87_MED1_11378_lociStitched chr16 76138395 76189426 2_U87_MED1_19517_lociStitched chr3 4992550 5013365 9_U87_MED1_24067_lociStitched chr5 90604451 90646666 6_U87_MED1_24844_lociStitched chr5 150121686 150155852 5_U87_MED1_27721_lociStitched chr7 72748931 72774831 10_U87_MED1_20211_lociStitched chr3 55151891 55214347 6_U87_MED1_5659_lociStitched chr11 64995165 65033129 3_U87_MED1_19044_lociStitched chr22 28920868 28939971 8_U87_MED1_24834_lociStitched chr5 149974547 150020460 13_U87_MED1_21089_lociStitched chr3 142532100 142623859 19_U87_MED1_18679_lociStitched chr21 38534163 38647146 11_U87_MED1_28206_lociStitched chr7 115938214 116016989 3_U87_MED1_12623_lociStitched chr17 55257387 55278945 15_U87_MED1_7069_lociStitched chr12 61372699 61474955 U87_MED1_5680 chr11 65411528 65428724 U87_MED1_5682 chr11 65433153 65444824 U87_MED1_19439 chr22 44836466 44869626 2_U87_MED1_3956_lociStitched chr10 73689550 73708761 4_U87_MED1_27840_lociStitched chr7 81067427 81109206 3_U87_MED1_32102_lociStitched chrX 45440741 45464841 5_U87_MED1_28952_lociStitched chr8 24104754 24143595 21_U87_MED1_5003_lociStitched chr11 12100995 12218222 11_U87_MED1_26945_lociStitched chr6 158359374 158413800 10_U87_MED1_3959_lociStitched chr10 73725225 73767483 5_U87_MED1_3340_lociStitched chr10 17280959 17321940 5_U87_MED1_11362_lociStitched chr16 75864680 75900842 4_U87_MED1_26256_lociStitched chr6 86210398 86250125 10_U87_MED1_8940_lociStitched chr14 61060615 61131816 7_U87_MED1_20945_lociStitched chr3 128935531 128978089 7_U87_MED1_9371_lociStitched chr14 95781765 95823179 7_U87_MED1_17803_lociStitched chr20 29638882 29664742 6_U87_MED1_11435_lociStitched chr16 81214233 81249274 8_U87_MED1_23347_lociStitched chr5 14195028 14261996 21_U87_MED1_25200_lociStitched chr5 172209298 172316383 6_U87_MED1_22301_lociStitched chr4 74786901 74829347 8_U87_MED1_31350_lociStitched chr9 117391466 117456436 2_U87_MED1_11091_lociStitched chr16 55196851 55207509 3_U87_MED1_16900_lociStitched chr2 207810793 207833238 14_U87_MED1_4025_lociStitched chr10 76895156 76977932 7_U87_MED1_7635_lociStitched chr12 119145594 119188677 15_U87_MED1_10048_lociStitched chr15 65153353 65230563 12_U87_MED1_27257_lociStitched chr7 22565898 22624022 1_U87_MED1_25943_lociStitched chr6 43843596 43867854 4_U87_MED1_5758_lociStitched chr11 68819807 68846515 3_U87_MED1_22330_lociStitched chr4 75290119 75317605 12_U87_MED1_9569_lociStitched chr15 30898025 30959213 14_U87_MED1_25174_lociStitched chr5 172116992 172191454 15_U87_MED1_29037_lociStitched chr8 28260823 28333470 5_U87_MED1_17455_lociStitched chr2 238996356 239014679 4_U87_MED1_22339_lociStitched chr4 75448510 75480580 2_U87_MED1_12177_lociStitched chr17 35423480 35437302 9_U87_MED1_19052_lociStitched chr22 28954187 29006184 5_U87_MED1_20569_lociStitched chr3 100162550 100188309 9_U87_MED1_23186_lociStitched chr4 189557679 189609237 11_U87_MED1_31536_lociStitched chr9 129340908 129389008 4_U87_MED1_23355_lociStitched chr5 14450202 14474301 U87_MED1_6146 chr11 121515959 121540976 8_U87_MED1_25729_lociStitched chr6 30816520 30858966 10_U87_MED1_4983_lociStitched chr11 12020084 12069159 16_U87_MED1_18248_lociStitched chr20 51915427 52011299 2_U87_MED1_23778_lociStitched chr5 64520345 64541781 9_U87_MED1_7528_lociStitched chr12 110318731 110366261 1_U87_MED1_7124_lociStitched chr12 64501251 64520825 12_U87_MED1_12963_lociStitched chr17 73791501 73869039 11_U87_MED1_19190_lociStitched chr22 35053881 35115041 10_U87_MED1_21395_lociStitched chr3 171889621 171955016 8_U87_MED1_1494_lociStitched chr1 94946918 94980513 11_U87_MED1_18744_lociStitched chr21 41905622 41959032 5_U87_MED1_16409_lociStitched chr2 160767297 160807533 7_U87_MED1_24782_lociStitched chr5 149368846 149428980 11_U87_MED1_30075_lociStitched chr8 128970951 129032504 7_U87_MED1_3670_lociStitched chr10 49466581 49513686 11_U87_MED1_96_lociStitched chr1 7976379 8045080 7_U87_MED1_18338_lociStitched chr20 58219251 58265651 7_U87_MED1_24799_lociStitched chr5 149623193 149663216 13_U87_MED1_31238_lociStitched chr9 113811355 113877599 11_U87_MED1_4127_lociStitched chr10 80528198 80590428 2_U87_MED1_26448_lociStitched chr6 112461732 112477579 7_U87_MED1_28103_lociStitched chr7 105771944 105806491 18_U87_MED1_31033_lociStitched chr9 100772868 100889180 14_U87_MED1_30675_lociStitched chr9 37974257 38060126 8_U87_MED1_10549_lociStitched chr15 99038601 99089992 11_U87_MED1_9182_lociStitched chr14 76439874 76498969 7_U87_MED1_24848_lociStitched chr5 150413621 150465246 6_U87_MED1_23363_lociStitched chr5 14492548 14555243 3_U87_MED1_13121_lociStitched chr18 3575542 3597033 12_U87_MED1_24585_lociStitched chr5 138995233 139071634 6_U87_MED1_5284_lociStitched chr11 35116090 35159659 8_U87_MED1_3521_lociStitched chr10 33284148 33345221 7_U87_MED1_3616_lociStitched chr10 43658240 43708520 13_U87_MED1_9361_lociStitched chr14 95621243 95685962 4_U87_MED1_1127_lociStitched chr1 58992223 59025064 7_U87_MED1_12194_lociStitched chr17 35693162 35742563 8_U87_MED1_16879_lociStitched chr2 206252656 206308088 9_U87_MED1_8736_lociStitched chr14 34901740 34946481 4_U87_MED1_31655_lociStitched chr9 132701910 132727822 9_U87_MED1_28850_lociStitched chr8 22269372 22319900 6_U87_MED1_1768_lociStitched chr1 143784496 143840429 4_U87_MED1_103_lociStitched chr1 8059282 8081510 7_U87_MED1_2854_lociStitched chr1 222980231 223015835 8_U87_MED1_10117_lociStitched chr15 68542055 68588784 7_U87_MED1_9901_lociStitched chr15 58441168 58488832 3_U87_MED1_15883_lociStitched chr2 101938979 101958391 3_U87_MED1_2303_lociStitched chr1 181502080 181517873 3_U87_MED1_9993_lociStitched chr15 63374614 63385055 5_U87_MED1_4927_lociStitched chr11 10276396 10310109 8_U87_MED1_152_lociStitched chr1 9145323 9194908 7_U87_MED1_9271_lociStitched chr14 90758863 90795031 5_U87_MED1_292_lociStitched chr1 16147097 16166359 9_U87_MED1_21428_lociStitched chr3 173326232 173383239 3_U87_MED1_1480_lociStitched chr1 94764000 94783945 8_U87_MED1_23764_lociStitched chr5 64362972 64408615 3_U87_MED1_29946_lociStitched chr8 123392549 123407278 7_U87_MED1_12906_lociStitched chr17 72195710 72225546 8_U87_MED1_15990_lociStitched chr2 113267162 113314982 7_U87_MED1_116_lociStitched chr1 8176575 8201970 5_U87_MED1_3649_lociStitched chr10 44783418 44814443 U87_MED1_12057 chr17 26944014 26950786 2_U87_MED1_28437_lociStitched chr7 137207368 137218994 5_U87_MED1_12467_lociStitched chr17 45458793 45498200 6_U87_MED1_7769_lociStitched chr12 123954906 123991790 8_U87_MED1_31230_lociStitched chr9 113739183 113777283 5_U87_MED1_31605_lociStitched chr9 131283335 131311945 7_U87_MED1_13271_lociStitched chr18 18500819 18546785 6_U87_MED1_11526_lociStitched chr16 85154494 85187872 6_U87_MED1_10162_lociStitched chr15 72000419 72046025 2_U87_MED1_23340_lociStitched chr5 14085673 14095662 2_U87_MED1_19978_lociStitched chr3 43871898 43892096 3_U87_MED1_6430_lociStitched chr12 6511065 6534804 9_U87_MED1_19998_lociStitched chr3 45053955 45084099 7_U87_MED1_16195_lociStitched chr2 134284761 134318932 11_U87_MED1_23940_lociStitched chr5 77835851 77885336 6_U87_MED1_27845_lociStitched chr7 81142953 81184064 4_U87_MED1_17882_lociStitched chr20 33353373 33372955 10_U87_MED1_28600_lociStitched chr7 154610962 154658753 5_U87_MED1_4664_lociStitched chr10 124030434 124058691 4_U87_MED1_31381_lociStitched chr9 118068405 118091501 3_U87_MED1_29735_lociStitched chr8 103869131 103893137 5_U87_MED1_10189_lociStitched chr15 72475467 72510666 10_U87_MED1_24811_lociStitched chr5 149818464 149877985 7_U87_MED1_30097_lociStitched chr8 129248470 129279733 3_U87_MED1_9036_lociStitched chr14 68314932 68333600 5_U87_MED1_20051_lociStitched chr3 46104252 46131876 4_U87_MED1_1138_lociStitched chr1 59085582 59122632 4_U87_MED1_15701_lociStitched chr2 75667467 75701638 4_U87_MED1_711_lociStitched chr1 33565656 33589393 8_U87_MED1_13446_lociStitched chr18 42508896 42556266 10_U87_MED1_30394_lociStitched chr9 3846346 3907818 3_U87_MED1_19433_lociStitched chr22 44770633 44789144 8_U87_MED1_12920_lociStitched chr17 72792423 72841736 3_U87_MED1_29401_lociStitched chr8 62831256 62843484 8_U87_MED1_23950_lociStitched chr5 77897945 77947772 4_U87_MED1_11532_lociStitched chr16 85244100 85274282 3_U87_MED1_17802_lociStitched chr20 29610545 29626036 9_U87_MED1_7003_lociStitched chr12 55806899 55852250 9_U87_MED1_30667_lociStitched chr9 37919181 37959597 5_U87_MED1_23475_lociStitched chr5 34599305 34646619 9_U87_MED1_21809_lociStitched chr4 5774565 5812219 5_U87_MED1_2484_lociStitched chr1 199931838 199958314 2_U87_MED1_18366_lociStitched chr20 60595254 60615120 3_U87_MED1_7103_lociStitched chr12 64204208 64218785 2_U87_MED1_20034_lociStitched chr3 45560540 45571271 3_U87_MED1_12304_lociStitched chr17 38789690 38802753 5_U87_MED1_22699_lociStitched chr4 123904338 123939922 4_U87_MED1_9736_lociStitched chr15 43521877 43538803 7_U87_MED1_11894_lociStitched chr17 16864733 16908403 5_U87_MED1_22347_lociStitched chr4 75606560 75632402 7_U87_MED1_3329_lociStitched chr10 17067573 17112416 7_U87_MED1_11080_lociStitched chr16 54061119 54092821 6_U87_MED1_3934_lociStitched chr10 73013845 73035645 8_U87_MED1_9304_lociStitched chr14 92160646 92214011 8_U87_MED1_131_lociStitched chr1 8851431 8891614 6_U87_MED1_2968_lociStitched chr1 232801400 232834869 7_U87_MED1_4111_lociStitched chr10 80355085 80408481 7_U87_MED1_6339_lociStitched chr12 2222492 2249299 4_U87_MED1_26068_lociStitched chr6 52475692 52496081 10_U87_MED1_27934_lociStitched chr7 93489372 93537292 5_U87_MED1_3808_lociStitched chr10 64315142 64346977 3_U87_MED1_944_lociStitched chr1 44945138 44970174 3_U87_MED1_18034_lociStitched chr20 43147144 43169721 3_U87_MED1_325_lociStitched chr1 17094881 17113779 3_U87_MED1_3042_lociStitched chr1 238461272 238489689 9_U87_MED1_1156_lociStitched chr1 59361216 59425669 6_U87_MED1_30197_lociStitched chr8 134210870 134248321 3_U87_MED1_32076_lociStitched chrX 43702439 43721105 8_U87_MED1_5161_lociStitched chr11 27864823 27914163 9_U87_MED1_2459_lociStitched chr1 199680258 199726111 4_U87_MED1_7235_lociStitched chr12 74697858 74717726 5_U87_MED1_4730_lociStitched chr10 127900118 127932927 6_U87_MED1_22320_lociStitched chr4 75178405 75219573 5_U87_MED1_7127_lociStitched chr12 64537567 64575468 4_U87_MED1_17184_lociStitched chr2 226993280 227021635 5_U87_MED1_16908_lociStitched chr2 207958570 207998045 5_U87_MED1_15976_lociStitched chr2 113096151 113124471 5_U87_MED1_19506_lociStitched chr3 4727890 4764151 1_U87_MED1_204_lociStitched chr1 11889850 11893062 3_U87_MED1_13789_lociStitched chr19 1198622 1219360 5_U87_MED1_4735_lociStitched chr10 128052098 128101696 5_U87_MED1_31406_lociStitched chr9 122171758 122206963 5_U87_MED1_9188_lociStitched chr14 76558717 76596203 2_U87_MED1_8973_lociStitched chr14 64612804 64614687 11_U87_MED1_18186_lociStitched chr20 49369237 49419385 2_U87_MED1_29678_lociStitched chr8 99439088 99452526 4_U87_MED1_5551_lociStitched chr11 61478002 61500583 10_U87_MED1_2485_lociStitched chr1 199971787 200011527 6_U87_MED1_3459_lociStitched chr10 29949767 29989251 7_U87_MED1_17938_lociStitched chr20 36229309 36280924 6_U87_MED1_21893_lociStitched chr4 13498370 13544429 5_U87_MED1_18845_lociStitched chr21 46282572 46307112 5_U87_MED1_28712_lociStitched chr8 11343022 11377910 5_U87_MED1_11837_lociStitched chr17 13568637 13595972 5_U87_MED1_26443_lociStitched chr6 112399077 112447095 10_U87_MED1_27794_lociStitched chr7 76875842 76933318 6_U87_MED1_3787_lociStitched chr10 63974312 64024395 3_U87_MED1_32094_lociStitched chrX 45249029 45269337 7_U87_MED1_2818_lociStitched chr1 221956329 221986465 1_U87_MED1_7642_lociStitched chr12 119212723 119216302 5_U87_MED1_15994_lociStitched chr2 113341276 113362882 5_U87_MED1_20226_lociStitched chr3 55462763 55499466 8_U87_MED1_25357_lociStitched chr5 179683140 179713756 10_U87_MED1_21194_lociStitched chr3 150772593 150825135 4_U87_MED1_19522_lociStitched chr3 5033023 5054218 4_U87_MED1_15905_lociStitched chr2 105378414 105401351 3_U87_MED1_17219_lociStitched chr2 228388427 228408117 2_U87_MED1_13120_lociStitched chr18 3436350 3456896 4_U87_MED1_3990_lociStitched chr10 75315563 75338505 4_U87_MED1_11024_lociStitched chr16 49738943 49767162 5_U87_MED1_770_lociStitched chr1 36580667 36626685 4_U87_MED1_719_lociStitched chr1 33647773 33674750 3_U87_MED1_24071_lociStitched chr5 90698489 90717110 12_U87_MED1_5468_lociStitched chr11 56798699 56850272 4_U87_MED1_15820_lociStitched chr2 99841615 99866659 4_U87_MED1_12059_lociStitched chr17 27024805 27048099 4_U87_MED1_19578_lociStitched chr3 10205559 10223302 9_U87_MED1_31314_lociStitched chr9 116906615 116969979 5_U87_MED1_17381_lociStitched chr2 237695304 237731727 4_U87_MED1_15023_lociStitched chr2 28463256 28486432 6_U87_MED1_16974_lociStitched chr2 216253277 216287004 6_U87_MED1_16311_lociStitched chr2 151031128 151061882 6_U87_MED1_3547_lociStitched chr10 33659030 33711377 5_U87_MED1_11814_lociStitched chr17 13181474 13210125 4_U87_MED1_28576_lociStitched chr7 151008488 151029657 1_U87_MED1_13124_lociStitched chr18 3611922 3616326 8_U87_MED1_3534_lociStitched chr10 33444568 33494188 6_U87_MED1_1871_lociStitched chr1 150209432 150241437 2_U87_MED1_18051_lociStitched chr20 43832868 43845622 3_U87_MED1_10146_lociStitched chr15 70301493 70317899 7_U87_MED1_2527_lociStitched chr1 201747626 201796040 13_U87_MED1_24272_lociStitched chr5 112383768 112458948 5_U87_MED1_26430_lociStitched chr6 112137473 112179561 4_U87_MED1_13429_lociStitched chr18 41626488 41662617 6_U87_MED1_8590_lociStitched chr13 113882656 113916801 9_U87_MED1_9551_lociStitched chr15 30738592 30802325 6_U87_MED1_17744_lociStitched chr20 23071349 23090627 6_U87_MED1_10416_lociStitched chr15 88161556 88193745 3_U87_MED1_5273_lociStitched chr11 35007450 35019639 2_U87_MED1_1556_lociStitched chr1 100859494 100870177 4_U87_MED1_29271_lociStitched chr8 49481932 49508141 5_U87_MED1_19225_lociStitched chr22 36029312 36057715 5_U87_MED1_29265_lociStitched chr8 49377506 49400335 10_U87_MED1_9028_lociStitched chr14 68199644 68255143 8_U87_MED1_12801_lociStitched chr17 67895139 67931773 2_U87_MED1_4101_lociStitched chr10 79683341 79694556 5_U87_MED1_16956_lociStitched chr2 215974532 216011850 6_U87_MED1_32082_lociStitched chrX 43746648 43786932 4_U87_MED1_18137_lociStitched chr20 48353990 48372553 1_U87_MED1_5584_lociStitched chr11 62363092 62367099 6_U87_MED1_15922_lociStitched chr2 108226124 108262222 5_U87_MED1_16864_lociStitched chr2 204370112 204385649 14_U87_MED1_16427_lociStitched chr2 160916322 160997972 8_U87_MED1_23630_lociStitched chr5 52329945 52369930 5_U87_MED1_17309_lociStitched chr2 234814049 234832679 U87_MED1_12055 chr17 26929956 26934384 6_U87_MED1_23098_lociStitched chr4 182794994 182847907 7_U87_MED1_2995_lociStitched chr1 233157788 233200699 4_U87_MED1_4147_lociStitched chr10 80745860 80764435 10_U87_MED1_25839_lociStitched chr6 35221878 35273955 2_U87_MED1_3179_lociStitched chr10 4794967 4808857 5_U87_MED1_12475_lociStitched chr17 45628535 45655344 3_U87_MED1_28098_lociStitched chr7 105697048 105714277 1_U87_MED1_23343_lociStitched chr5 14157879 14165158 6_U87_MED1_20739_lociStitched chr3 113836451 113858193 6_U87_MED1_2468_lociStitched chr1 199766249 199799338 4_U87_MED1_4913_lociStitched chr11 9730174 9767132 2_U87_MED1_20084_lociStitched chr3 48567365 48579540 6_U87_MED1_28721_lociStitched chr8 11390711 11411534 5_U87_MED1_7081_lociStitched chr12 62839721 62868417 4_U87_MED1_23208_lociStitched chr4 190929117 190951845 8_U87_MED1_15178_lociStitched chr2 37846146 37884311 5_U87_MED1_9939_lociStitched chr15 60965417 60980962 9_U87_MED1_18605_lociStitched chr21 35076849 35141236 7_U87_MED1_9763_lociStitched chr15 46746824 46776787 3_U87_MED1_27564_lociStitched chr7 45880224 45893741 5_U87_MED1_28912_lociStitched chr8 23294269 23325787 2_U87_MED1_4059_lociStitched chr10 78777531 78788869 5_U87_MED1_23069_lociStitched chr4 178139337 178175485 3_U87_MED1_12646_lociStitched chr17 56755482 56771755 3_U87_MED1_16239_lociStitched chr2 143331502 143355637 3_U87_MED1_29002_lociStitched chr8 26540715 26557275 6_U87_MED1_29815_lociStitched chr8 116499299 116540088 6_U87_MED1_31373_lociStitched chr9 118032147 118053805 4_U87_MED1_1780_lociStitched chr1 144138664 144168151 5_U87_MED1_30166_lociStitched chr8 132922317 132943207 9_U87_MED1_30246_lociStitched chr8 134963771 135009147 3_U87_MED1_23445_lociStitched chr5 33334716 33357539 6_U87_MED1_17250_lociStitched chr2 230173938 230207111 5_U87_MED1_18788_lociStitched chr21 43737139 43761842 6_U87_MED1_26457_lociStitched chr6 112629871 112666312 6_U87_MED1_12208_lociStitched chr17 35930846 35971407 9_U87_MED1_28935_lociStitched chr8 23632043 23677190 6_U87_MED1_15610_lociStitched chr2 72004300 72031901 4_U87_MED1_28289_lociStitched chr7 128254122 128269877 1_U87_MED1_5182_lociStitched chr11 28810629 28817709 2_U87_MED1_18609_lociStitched chr21 35174645 35187060 5_U87_MED1_28350_lociStitched chr7 130960595 130990571 4_U87_MED1_22927_lociStitched chr4 158071384 158094259 5_U87_MED1_4012_lociStitched chr10 76826281 76861798 7_U87_MED1_379_lociStitched chr1 19621887 19652224 6_U87_MED1_18585_lociStitched chr21 34818327 34848489 5_U87_MED1_904_lociStitched chr1 43160882 43182066 2_U87_MED1_15586_lociStitched chr2 70676208 70689547 2_U87_MED1_31394_lociStitched chr9 118343216 118354200 1_U87_MED1_23352_lociStitched chr5 14316952 14324472 10_U87_MED1_19673_lociStitched chr3 14426598 14490180 6_U87_MED1_4067_lociStitched chr10 78929913 78962884 4_U87_MED1_29950_lociStitched chr8 123509564 123529619 4_U87_MED1_31528_lociStitched chr9 129297192 129326262 4_U87_MED1_20561_lociStitched chr3 100091920 100125071 5_U87_MED1_28581_lociStitched chr7 151055255 151084698 5_U87_MED1_26426_lociStitched chr6 111980027 112035051 2_U87_MED1_18956_lociStitched chr22 23149440 23163217 2_U87_MED1_1656_lociStitched chr1 112077002 112088768 4_U87_MED1_15603_lociStitched chr2 71956835 71971756 3_U87_MED1_30321_lociStitched chr8 145079732 145099991 3_U87_MED1_233_lociStitched chr1 12575481 12603692 6_U87_MED1_28749_lociStitched chr8 13254372 13279984 7_U87_MED1_1977_lociStitched chr1 154332675 154367183 2_U87_MED1_18293_lociStitched chr20 56022630 56028783 9_U87_MED1_886_lociStitched chr1 41966619 42023301 6_U87_MED1_16981_lociStitched chr2 216300355 216347664 6_U87_MED1_28927_lociStitched chr8 23451758 23481764 1_U87_MED1_30073_lociStitched chr8 128932139 128937025 5_U87_MED1_19816_lociStitched chr3 27537533 27571776 7_U87_MED1_7805_lociStitched chr12 126597650 126639572 5_U87_MED1_25946_lociStitched chr6 43985976 44003858 3_U87_MED1_28109_lociStitched chr7 105844701 105854365 2_U87_MED1_9252_lociStitched chr14 89810151 89818908 4_U87_MED1_27267_lociStitched chr7 22723409 22739542 13_U87_MED1_28793_lociStitched chr8 19068482 19131291 6_U87_MED1_5481_lociStitched chr11 56930199 56959561 2_U87_MED1_27568_lociStitched chr7 45915902 45931369 6_U87_MED1_4303_lociStitched chr10 95208065 95226275 7_U87_MED1_7132_lociStitched chr12 64596525 64639788 6_U87_MED1_16065_lociStitched chr2 121175738 121225198 U87_MED1_14366 chr19 47304243 47311641 7_U87_MED1_18808_lociStitched chr21 43994975 44024520 2_U87_MED1_5008_lociStitched chr11 12259582 12267357 4_U87_MED1_26112_lociStitched chr6 56306428 56344388 2_U87_MED1_3174_lociStitched chr10 4694138 4705791 7_U87_MED1_17815_lociStitched chr20 29747030 29779683 4_U87_MED1_8309_lociStitched chr13 79502139 79529052 8_U87_MED1_15724_lociStitched chr2 84968849 85007114 5_U87_MED1_24412_lociStitched chr5 131448786 131468778 6_U87_MED1_3854_lociStitched chr10 69512331 69537255 4_U87_MED1_14415_lociStitched chr19 49931469 49950265 5_U87_MED1_14037_lociStitched chr19 13121190 13144815 4_U87_MED1_7978_lociStitched chr13 32722777 32758954 6_U87_MED1_8934_lociStitched chr14 60998858 61027173 1_U87_MED1_31355_lociStitched chr9 117490731 117497452 4_U87_MED1_16010_lociStitched chr2 113713570 113730597 8_U87_MED1_29905_lociStitched chr8 120625584 120684952 1_U87_MED1_12621_lociStitched chr17 55214356 55220009 4_U87_MED1_18033_lociStitched chr20 43105683 43130852 1_U87_MED1_14566_lociStitched chr19 56760348 56770942 3_U87_MED1_6635_lociStitched chr12 26157496 26179828 10_U87_MED1_26800_lociStitched chr6 148859778 148930005 11_U87_MED1_3404_lociStitched chr10 24761351 24796199 U87_MED1_6149 chr11 121571509 121574883 4_U87_MED1_30210_lociStitched chr8 134368437 134385618 6_U87_MED1_1544_lociStitched chr1 99882905 99924721 5_U87_MED1_12392_lociStitched chr17 42688819 42727303 8_U87_MED1_20455_lociStitched chr3 72114549 72164267 9_U87_MED1_28371_lociStitched chr7 133767195 133816793 4_U87_MED1_1833_lociStitched chr1 148842282 148859888 1_U87_MED1_16194_lociStitched chr2 134260935 134266764 5_U87_MED1_3298_lociStitched chr10 14467377 14497715 5_U87_MED1_19494_lociStitched chr3 4417975 4444229 5_U87_MED1_23525_lociStitched chr5 37806374 37829663 7_U87_MED1_20638_lociStitched chr3 103127775 103167026 5_U87_MED1_15026_lociStitched chr2 28518271 28546447 5_U87_MED1_24346_lociStitched chr5 121505170 121548141 1_U87_MED1_72_lociStitched chr1 7279930 7284880 2_U87_MED1_22344_lociStitched chr4 75583830 75590802 2_U87_MED1_19612_lociStitched chr3 11295015 11308874 5_U87_MED1_6644_lociStitched chr12 26315522 26344028 4_U87_MED1_18578_lociStitched chr21 34262111 34276116 3_U87_MED1_16960_lociStitched chr2 216100277 216111305 3_U87_MED1_11901_lociStitched chr17 16984314 17001391 3_U87_MED1_5664_lociStitched chr11 65079515 65090536 4_U87_MED1_14346_lociStitched chr19 46416158 46427894 2_U87_MED1_24022_lociStitched chr5 86448382 86461105 3_U87_MED1_12721_lociStitched chr17 61694793 61709067 6_U87_MED1_24200_lociStitched chr5 106725129 106753981 11_U87_MED1_25306_lociStitched chr5 177709555 177748817 7_U87_MED1_13705_lociStitched chr18 66175119 66216988 5_U87_MED1_14892_lociStitched chr2 20229043 20250537 5_U87_MED1_358_lociStitched chr1 18060509 18078661 8_U87_MED1_29868_lociStitched chr8 119059307 119101868 2_U87_MED1_31353_lociStitched chr9 117468982 117476962 4_U87_MED1_26509_lociStitched chr6 117867944 117880133 4_U87_MED1_6791_lociStitched chr12 45948501 45963507 1_U87_MED1_7316_lociStitched chr12 88263372 88272888 1_U87_MED1_28454_lociStitched chr7 139014545 139019742 3_U87_MED1_29676_lociStitched chr8 99413377 99423302 6_U87_MED1_23651_lociStitched chr5 52728355 52762900 4_U87_MED1_29126_lociStitched chr8 32294513 32321547 1_U87_MED1_16937_lociStitched chr2 213414737 213420189 5_U87_MED1_9017_lociStitched chr14 68071320 68092309 2_U87_MED1_7050_lociStitched chr12 61281616 61290216 2_U87_MED1_8479_lociStitched chr13 105600869 105608876 3_U87_MED1_28991_lociStitched chr8 26361671 26378373 9_U87_MED1_3200_lociStitched chr10 5566940 5627226 3_U87_MED1_30976_lociStitched chr9 96662387 96672240 4_U87_MED1_29291_lociStitched chr8 49966143 50006378 6_U87_MED1_9106_lociStitched chr14 72173702 72203999 8_U87_MED1_16377_lociStitched chr2 158024751 158054345 5_U87_MED1_21864_lociStitched chr4 9775313 9798168 4_U87_MED1_11370_lociStitched chr16 75998735 76031950 7_U87_MED1_15218_lociStitched chr2 39560078 39595092 8_U87_MED1_12696_lociStitched chr17 59756987 59812906 8_U87_MED1_25005_lociStitched chr5 159233084 159273365 2_U87_MED1_14996_lociStitched chr2 27872924 27887411 1_U87_MED1_9389_lociStitched chr14 96712814 96717531 5_U87_MED1_27903_lociStitched chr7 92088104 92112431 7_U87_MED1_4679_lociStitched chr10 124239479 124271216 6_U87_MED1_30005_lociStitched chr8 125807278 125854903 6_U87_MED1_28456_lociStitched chr7 139069397 139084495 2_U87_MED1_24155_lociStitched chr5 97670802 97679322 8_U87_MED1_21597_lociStitched chr3 189462566 189498548 6_U87_MED1_11827_lociStitched chr17 13364635 13408579 7_U87_MED1_3680_lociStitched chr10 50039199 50063569 2_U87_MED1_19061_lociStitched chr22 29134450 29153278 3_U87_MED1_23518_lociStitched chr5 37750719 37760798 3_U87_MED1_7310_lociStitched chr12 88073577 88084969 1_U87_MED1_13590_lociStitched chr18 54176974 54185409 8_U87_MED1_8053_lociStitched chr13 42279138 42321467 4_U87_MED1_12184_lociStitched chr17 35505423 35524108 4_U87_MED1_13264_lociStitched chr18 18384075 18398874 2_U87_MED1_9121_lociStitched chr14 72995992 73005780 1_U87_MED1_318_lociStitched chr1 16712459 16713704 4_U87_MED1_28428_lociStitched chr7 136991184 137032443 1_U87_MED1_21899_lociStitched chr4 13595377 13602846 6_U87_MED1_1236_lociStitched chr1 66500300 66532014 2_U87_MED1_23649_lociStitched chr5 52691426 52701566 2_U87_MED1_1146_lociStitched chr1 59278815 59285007 3_U87_MED1_4738_lociStitched chr10 128136077 128148428 1_U87_MED1_16895_lociStitched chr2 207733794 207741019 U87_MED1_6147 chr11 121541171 121547835 8_U87_MED1_18611_lociStitched chr21 35259187 35300591 5_U87_MED1_21690_lociStitched chr3 195673864 195696713 6_U87_MED1_24681_lociStitched chr5 142535854 142577824 4_U87_MED1_25215_lociStitched chr5 172809327 172835222 4_U87_MED1_14706_lociStitched chr2 9220694 9250055 5_U87_MED1_17204_lociStitched chr2 227939599 227962404 8_U87_MED1_28194_lociStitched chr7 115849254 115893839 5_U87_MED1_19772_lociStitched chr3 23665020 23703368 3_U87_MED1_15004_lociStitched chr2 28029902 28039153 4_U87_MED1_106_lociStitched chr1 8103590 8124963 5_U87_MED1_817_lociStitched chr1 39625358 39648692 6_U87_MED1_28612_lociStitched chr7 154678056 154722945 7_U87_MED1_432_lociStitched chr1 21495634 21538118 2_U87_MED1_31267_lociStitched chr9 115421719 115435645 7_U87_MED1_12576_lociStitched chr17 53290132 53326319 6_U87_MED1_19801_lociStitched chr3 25588763 25621509 3_U87_MED1_27050_lociStitched chr7 183514 197682 9_U87_MED1_14480_lociStitched chr19 52127006 52186848 6_U87_MED1_19418_lociStitched chr22 44358335 44388085 2_U87_MED1_30163_lociStitched chr8 132894337 132909622 U87_MED1_14367 chr19 47316482 47321267 4_U87_MED1_12273_lociStitched chr17 37922830 37933478 5_U87_MED1_24689_lociStitched chr5 142592522 142623091 4_U87_MED1_20269_lociStitched chr3 58004870 58021097 3_U87_MED1_27523_lociStitched chr7 43645607 43666145 1_U87_MED1_17177_lociStitched chr2 226687043 226693005 2_U87_MED1_6543_lociStitched chr12 13239108 13252365 5_U87_MED1_17087_lociStitched chr2 220013772 220043266 1_U87_MED1_30069_lociStitched chr8 128815091 128825309 4_U87_MED1_29371_lociStitched chr8 59816874 59844700 1_U87_MED1_6537_lociStitched chr12 13141485 13148287 7_U87_MED1_5290_lociStitched chr11 35188819 35225440 2_U87_MED1_27570_lociStitched chr7 45982964 45992590 2_U87_MED1_14283_lociStitched chr19 43180211 43188202 4_U87_MED1_15878_lociStitched chr2 101801067 101827913 7_U87_MED1_3818_lociStitched chr10 64389081 64435800 1_U87_MED1_1809_lociStitched chr1 148122343 148127505 7_U87_MED1_4527_lociStitched chr10 112142380 112177089 3_U87_MED1_779_lociStitched chr1 37709463 37726142 3_U87_MED1_28080_lociStitched chr7 104399029 104413643 8_U87_MED1_18902_lociStitched chr22 19188215 19237227 2_U87_MED1_16544_lociStitched chr2 173720790 173735078 3_U87_MED1_14022_lociStitched chr19 12749117 12766578 4_U87_MED1_1829_lociStitched chr1 148799756 148819583 3_U87_MED1_1539_lociStitched chr1 99827254 99845083 3_U87_MED1_4484_lociStitched chr10 106077029 106101948 5_U87_MED1_30974_lociStitched chr9 96582128 96608518 5_U87_MED1_8539_lociStitched chr13 109840351 109863235 2_U87_MED1_21146_lociStitched chr3 147358174 147368300 3_U87_MED1_13125_lociStitched chr18 3638374 3656877 6_U87_MED1_24416_lociStitched chr5 131578682 131630139 6_U87_MED1_27818_lociStitched chr7 80166238 80194389 4_U87_MED1_31023_lociStitched chr9 100662763 100685315 2_U87_MED1_15229_lociStitched chr2 40176624 40187049

TABLE 4 SCLC Super-Enhancers Based on Gene Build hg 18 REGION_ID CHROM START STOP 1_H2171_MED1_1_1640_lociStitched chr12 6920935 6927602 3_H2171_MED1_1_4743_lociStitched chr20 20467079 20497912 7_H2171_MED1_1_1324_lociStitched chr11 44999379 45032693 7_H2171_MED1_1_4739_lociStitched chr20 20368291 20422337 3_H2171_MED1_1_4728_lociStitched chr20 20127551 20146821 5_H2171_MED1_1_2525_lociStitched chr14 100006544 100041089 10_H2171_MED1_1_1318_lociStitched chr11 44914282 44976798 7_H2171_MED1_1_3367_lociStitched chr17 52974161 53020737 5_H2171_MED1_1_2568_lociStitched chr14 105386944 105407220 4_H2171_MED1_1_2193_lociStitched chr13 70984696 70997790 4_H2171_MED1_1_1411_lociStitched chr11 65001189 65034088 5_H2171_MED1_1_2727_lociStitched chr15 67058222 67081109 4_H2171_MED1_1_4448_lociStitched chr2 182187487 182216832 2_H2171_MED1_1_3306_lociStitched chr17 38792864 38802484 7_H2171_MED1_1_3117_lociStitched chr16 84027236 84077758 4_H2171_MED1_1_2523_lociStitched chr14 99952877 99984071 4_H2171_MED1_1_6398_lociStitched chr6 20798985 20817496 1_H2171_MED1_1_5368_lociStitched chr3 73242222 73243091 2_H2171_MED1_1_1409_lociStitched chr11 64938799 64950566 10_H2171_MED1_1_5063_lociStitched chr22 28420926 28471660 3_H2171_MED1_1_1518_lociStitched chr11 110675092 110687227 2_H2171_MED1_1_106_lociStitched chr1 17094879 17105111 7_H2171_MED1_1_370_lociStitched chr1 61124688 61164318 3_H2171_MED1_1_4670_lociStitched chr20 5763423 5778470 3_H2171_MED1_1_2458_lociStitched chr14 80493803 80524114 2_H2171_MED1_1_2703_lociStitched chr15 63374895 63384854 2_H2171_MED1_1_196_lociStitched chr1 27718317 27729348 1_H2171_MED1_1_1626_lociStitched chr12 1909405 1917933 1_H2171_MED1_1_2022_lociStitched chr12 119212791 119216166 7_H2171_MED1_1_2994_lociStitched chr16 48115499 48154218 1_H2171_MED1_1_1385_lociStitched chr11 62364199 62367040 3_H2171_MED1_1_355_lociStitched chr1 60460911 60473852 8_H2171_MED1_1_4077_lociStitched chr2 50900527 50957040 3_H2171_MED1_1_4992_lociStitched chr21 45354314 45373451 3_H2171_MED1_1_4776_lociStitched chr20 29744744 29765111 1_H2171_MED1_1_86_lociStitched chr1 11890040 11892976 1_H2171_MED1_1_4772_lociStitched chr20 29655198 29660784 1_H2171_MED1_1_1806_lociStitched chr12 55914077 55924333 6_H2171_MED1_1_4832_lociStitched chr20 44860383 44878078 7_H2171_MED1_1_2352_lociStitched chr14 54625929 54653893 4_H2171_MED1_1_2589_lociStitched chr15 29345063 29360788 9_H2171_MED1_1_1076_lociStitched chr10 80658480 80712619 2_H2171_MED1_1_6438_lociStitched chr6 26263284 26281349 5_H2171_MED1_1_4748_lociStitched chr20 20518980 20554248 3_H2171_MED1_1_1797_lociStitched chr12 53731066 53749016 5_H2171_MED1_1_259_lociStitched chr1 41603873 41629260 2_H2171_MED1_1_4451_lociStitched chr2 182245805 182255349 7_H2171_MED1_1_4066_lociStitched chr2 50831888 50874042 3_H2171_MED1_1_1331_lociStitched chr11 45063502 45081811 3_H2171_MED1_1_7960_lociStitched chr9 131283833 131300537 1_H2171_MED1_1_3376_lociStitched chr17 54062985 54065019 2_H2171_MED1_1_3964_lociStitched chr2 8734984 8744081 1_H2171_MED1_1_844_lociStitched chr1 232925154 232930496 2_H2171_MED1_1_3925_lociStitched chr2 2305821 2317044 1_H2171_MED1_1_7716_lociStitched chr9 72222711 72226329 1_H2171_MED1_1_3377_lociStitched chr17 54090881 54092427 1_H2171_MED1_1_2879_lociStitched chr16 2456826 2462820 3_H2171_MED1_1_2486_lociStitched chr14 90046046 90059450 3_H2171_MED1_1_6363_lociStitched chr6 17580996 17600893 4_H2171_MED1_1_2646_lociStitched chr15 44378691 44396308 3_H2171_MED1_1_7981_lociStitched chr9 133669354 133683692 5_H2171_MED1_1_7401_lociStitched chr8 63107445 63135528 2_H2171_MED1_1_873_lociStitched chr1 241942356 241953358 1_H2171_MED1_1_1285_lociStitched chr11 31851717 31855125 4_H2171_MED1_1_7215_lociStitched chr7 127256053 127272711 4_H2171_MED1_1_2597_lociStitched chr15 29404315 29442687 2_H2171_MED1_1_4761_lociStitched chr20 24646465 24652204 3_H2171_MED1_1_4781_lociStitched chr20 30575765 30589140 2_H2171_MED1_1_3111_lociStitched chr16 83975326 83989531 4_H2171_MED1_1_488_lociStitched chr1 116596631 116613122 3_H2171_MED1_1_7399_lociStitched chr8 62993333 63023912 4_H2171_MED1_1_4597_lociStitched chr2 232245138 232257967 5_H2171_MED1_1_1703_lociStitched chr12 28479296 28497904 4_H2171_MED1_1_8014_lociStitched chr9 136814438 136833329 2_H2171_MED1_1_2533_lociStitched chr14 100108519 100126673 5_H2171_MED1_1_6671_lociStitched chr6 112078789 112091156 3_H2171_MED1_1_6930_lociStitched chr7 31684707 31699272 2_H2171_MED1_1_277_lociStitched chr1 44959548 44969924 1_H2171_MED1_1_4770_lociStitched chr20 29623515 29626066 3_H2171_MED1_1_3229_lociStitched chr17 18824205 18838508 5_H2171_MED1_1_7373_lociStitched chr8 53305190 53330760 2_H2171_MED1_1_4445_lociStitched chr2 182146929 182160614 5_H2171_MED1_1_6182_lociStitched chr5 142369672 142397549 3_H2171_MED1_1_3109_lociStitched chr16 83939477 83957133 1_H2171_MED1_1_6436_lociStitched chr6 26230266 26234969 2_H2171_MED1_1_5573_lociStitched chr3 171666644 171672601 4_H2171_MED1_1_7990_lociStitched chr9 133870805 133889409 7_H2171_MED1_1_324_lociStitched chr1 54535842 54595884 3_H2171_MED1_1_4733_lociStitched chr20 20330857 20340022 1_H2171_MED1_1_1286_lociStitched chr11 31970692 31975143 3_H2171_MED1_1_6477_lociStitched chr6 33819339 33828849 4_H2171_MED1_1_5144_lociStitched chr22 41520431 41540832 2_H2171_MED1_1_5576_lociStitched chr3 171727766 171734092 3_H2171_MED1_1_7552_lociStitched chr8 125856085 125872149 3_H2171_MED1_1_7535_lociStitched chr8 123754555 123765925 3_H2171_MED1_1_5948_lociStitched chr5 14793111 14810119 2_H2171_MED1_1_5868_lociStitched chr4 141377946 141394403 2_H2171_MED1_1_1526_lociStitched chr11 110802193 110813715 1_H2171_MED1_1_3506_lociStitched chr17 75396929 75402414 4_H2171_MED1_1_4283_lociStitched chr2 134996095 135011003 3_H2171_MED1_1_6663_lociStitched chr6 111978600 111995752 3_H2171_MED1_1_858_lociStitched chr1 235546011 235556631 1_H2171_MED1_1_3207_lociStitched chr17 8016708 8018589 4_H2171_MED1_1_303_lociStitched chr1 53346865 53379175 3_H2171_MED1_1_6854_lociStitched chr7 3273583 3282459 4_H2171_MED1_1_2201_lociStitched chr13 71269244 71287635 2_H2171_MED1_1_5514_lociStitched chr3 141542495 141547705 1_H2171_MED1_1_102_lociStitched chr1 16712502 16713836 1_H2171_MED1_1_3304_lociStitched chr17 38747760 38749588 4_H2171_MED1_1_3851_lociStitched chr19 43240289 43257408 3_H2171_MED1_1_7984_lociStitched chr9 133750060 133767255 2_H2171_MED1_1_2593_lociStitched chr15 29374833 29382092 4_H2171_MED1_1_1632_lociStitched chr12 3191844 3208689 3_H2171_MED1_1_613_lociStitched chr1 181446125 181455812 1_H2171_MED1_1_515_lociStitched chr1 147489769 147491715 1_H2171_MED1_1_7564_lociStitched chr8 127859208 127871721 2_H2171_MED1_1_4141_lociStitched chr2 70212694 70224525 1_H2171_MED1_1_3928_lociStitched chr2 2827367 2830692 3_H2171_MED1_1_3104_lociStitched chr16 83865721 83879079 3_H2171_MED1_1_7998_lociStitched chr9 134078841 134097047 3_H2171_MED1_1_7465_lociStitched chr8 93687205 93693913 3_H2171_MED1_1_2733_lociStitched chr15 67212499 67237556 4_H2171_MED1_1_2715_lociStitched chr15 64230622 64250211 2_H2171_MED1_1_1770_lociStitched chr12 48729670 48733984 5_H2171_MED1_1_5251_lociStitched chr3 16817691 16841285 2_H2171_MED1_1_8026_lociStitched chr9 137161098 137170211 4_H2171_MED1_1_5775_lociStitched chr4 80519421 80536721 3_H2171_MED1_1_4835_lociStitched chr20 45030700 45042538 2_H2171_MED1_1_5461_lociStitched chr3 127738334 127747382 1_H2171_MED1_1_3360_lociStitched chr17 52949374 52952330 3_H2171_MED1_1_4792_lociStitched chr20 31606072 31629076 3_H2171_MED1_1_5099_lociStitched chr22 36154719 36175974 3_H2171_MED1_1_3453_lociStitched chr17 69839454 69850658 2_H2171_MED1_1_606_lociStitched chr1 180846204 180855565 3_H2171_MED1_1_2977_lociStitched chr16 47549993 47564543 5_H2171_MED1_1_5509_lociStitched chr3 141387464 141408827 4_H2171_MED1_1_6832_lociStitched chr7 1281279 1305738 3_H2171_MED1_1_7419_lociStitched chr8 64128807 64152294 3_H2171_MED1_1_392_lociStitched chr1 67883445 67891831 3_H2171_MED1_1_7851_lociStitched chr9 111073312 111081518 1_H2171_MED1_1_3482_lociStitched chr17 73307672 73311962 1_H2171_MED1_1_677_lociStitched chr1 200341028 200344953 4_H2171_MED1_1_2770_lociStitched chr15 72303789 72325673 1_H2171_MED1_1_1390_lociStitched chr11 63440196 63445356 5_H2171_MED1_1_5682_lociStitched chr4 8071726 8098132 2_H2171_MED1_1_358_lociStitched chr1 60514461 60520511 2_H2171_MED1_1_8028_lociStitched chr9 137386784 137396443 4_H2171_MED1_1_4955_lociStitched chr21 38139981 38165165 6_H2171_MED1_1_1142_lociStitched chr10 112592513 112615109 4_H2171_MED1_1_672_lociStitched chr1 200253434 200274407 2_H2171_MED1_1_1016_lociStitched chr10 73690165 73706428 3_H2171_MED1_1_5762_lociStitched chr4 80338728 80352494 2_H2171_MED1_1_6852_lociStitched chr7 3187356 3195840 2_H2171_MED1_1_4985_lociStitched chr21 44518734 44524811 3_H2171_MED1_1_4943_lociStitched chr21 33430682 33447308 1_H2171_MED1_1_3368_lociStitched chr17 53035354 53040644 4_H2171_MED1_1_2427_lociStitched chr14 76442631 76461700 4_H2171_MED1_1_4558_lociStitched chr2 217169924 217196187 3_H2171_MED1_1_7744_lociStitched chr9 85109090 85122979 5_H2171_MED1_1_1691_lociStitched chr12 28264210 28281514 3_H2171_MED1_1_2892_lociStitched chr16 11047692 11059849 2_H2171_MED1_1_4899_lociStitched chr20 60880400 60885360 1_H2171_MED1_1_7947_lociStitched chr9 129461873 129464518 2_H2171_MED1_1_674_lociStitched chr1 200292057 200306846 2_H2171_MED1_1_2203_lociStitched chr13 71325559 71338429 2_H2171_MED1_1_3186_lociStitched chr17 3729010 3741942 2_H2171_MED1_1_2909_lociStitched chr16 11781980 11794751 2_H2171_MED1_1_4766_lociStitched chr20 25613739 25620530 3_H2171_MED1_1_2897_lociStitched chr16 11144367 11154452 1_H2171_MED1_1_5910_lociStitched chr5 451422 454266 4_H2171_MED1_1_7415_lociStitched chr8 63776687 63806155 1_H2171_MED1_1_1453_lociStitched chr11 78328712 78331262 3_H2171_MED1_1_6678_lociStitched chr6 112348676 112356273 2_H2171_MED1_1_1765_lociStitched chr12 48546951 48555151 1_H2171_MED1_1_2433_lociStitched chr14 76568042 76570777 1_H2171_MED1_1_7993_lociStitched chr9 133904790 133908837 2_H2171_MED1_1_3164_lociStitched chr17 1642357 1647888 4_H2171_MED1_1_1653_lociStitched chr12 8501768 8523291 2_H2171_MED1_1_8030_lociStitched chr9 138135585 138142078 4_H2171_MED1_1_6697_lociStitched chr6 114858043 114874406 2_H2171_MED1_1_2731_lociStitched chr15 67146253 67153108 1_H2171_MED1_1_676_lociStitched chr1 200320223 200323463 3_H2171_MED1_1_7106_lociStitched chr7 90891248 90904646 3_H2171_MED1_1_1282_lociStitched chr11 31605924 31622763 1_H2171_MED1_1_6439_lociStitched chr6 26304930 26308840 3_H2171_MED1_1_6542_lociStitched chr6 43874271 43891627 2_H2171_MED1_1_362_lociStitched chr1 61095855 61105484 3_H2171_MED1_1_4288_lociStitched chr2 135067807 135078675 1_H2171_MED1_1_2649_lociStitched chr15 44422399 44425293 4_H2171_MED1_1_1859_lociStitched chr12 74259275 74282803 2_H2171_MED1_1_6347_lociStitched chr6 15255876 15261598 3_H2171_MED1_1_3953_lociStitched chr2 7321393 7328314 1_H2171_MED1_1_3540_lociStitched chr17 77837805 77840024 2_H2171_MED1_1_6860_lociStitched chr7 5429395 5446166 2_H2171_MED1_1_3999_lociStitched chr2 23567475 23572888 1_H2171_MED1_1_5475_lociStitched chr3 130776820 130781469 1_H2171_MED1_1_4528_lociStitched chr2 207882381 207885158 2_H2171_MED1_1_842_lociStitched chr1 232900985 232903673 2_H2171_MED1_1_3986_lociStitched chr2 20412482 20420065 2_H2171_MED1_1_3326_lociStitched chr17 43434796 43447830 3_H2171_MED1_1_5929_lociStitched chr5 8720521 8737555 2_H2171_MED1_1_4569_lociStitched chr2 218968606 218980938 3_H2171_MED1_1_890_lociStitched chr10 1486532 1493897 1_H2171_MED1_1_7959_lociStitched chr9 131260227 131263591 3_H2171_MED1_1_2166_lociStitched chr13 58914764 58925684 1_H2171_MED1_1_8018_lociStitched chr9 136926589 136930226 4_H2171_MED1_1_3837_lociStitched chr19 40215562 40239946 2_H2171_MED1_1_6546_lociStitched chr6 43906068 43912657 1_H2171_MED1_1_331_lociStitched chr1 54796212 54799014 2_H2171_MED1_1_1637_lociStitched chr12 3677173 3687680 2_H2171_MED1_1_4907_lociStitched chr20 61600274 61610725 1_H2171_MED1_1_4771_lociStitched chr20 29638614 29640239 1_H2171_MED1_1_6475_lociStitched chr6 33043033 33048720 4_H2171_MED1_1_6405_lociStitched chr6 21296380 21310734 2_H2171_MED1_1_5758_lociStitched chr4 80183595 80191861 1_H2171_MED1_1_7556_lociStitched chr8 126466494 126468843 2_H2171_MED1_1_4002_lociStitched chr2 23606108 23613290 2_H2171_MED1_1_2058_lociStitched chr12 123805217 123810213 2_H2171_MED1_1_849_lociStitched chr1 233312827 233321459 3_H2171_MED1_1_3899_lociStitched chr19 53527025 53546826 2_H2171_MED1_1_395_lociStitched chr1 67912539 67916665 4_H2171_MED1_1_6138_lociStitched chr5 134851883 134865995 2_H2171_MED1_1_4060_lociStitched chr2 50612904 50617830 2_H2171_MED1_1_4365_lociStitched chr2 155710278 155720040 2_H2171_MED1_1_7889_lociStitched chr9 119201834 119207212 1_H2171_MED1_1_7587_lociStitched chr8 134455564 134458775 3_H2171_MED1_1_2601_lociStitched chr15 29458295 29478793 3_H2171_MED1_1_1260_lociStitched chr11 22313265 22322600 3_H2171_MED1_1_5218_lociStitched chr3 10469904 10487109 3_H2171_MED1_1_6827_lociStitched chr7 1204071 1217969 5_H2171_MED1_1_2046_lociStitched chr12 123556670 123583312 2_H2171_MED1_1_193_lociStitched chr1 27053645 27065430 2_H2171_MED1_1_4672_lociStitched chr20 5798497 5808334 4_H2171_MED1_1_1335_lociStitched chr11 45327480 45350583 2_H2171_MED1_1_3922_lociStitched chr2 1989631 2000522 3_H2171_MED1_1_1783_lociStitched chr12 51552711 51560557 1_H2171_MED1_1_4572_lociStitched chr2 219568763 219574266 1_H2171_MED1_1_8038_lociStitched chr9 138634973 138640138 2_H2171_MED1_1_450_lociStitched chr1 107836814 107840728 1_H2171_MED1_1_6340_lociStitched chr6 15092300 15095311 1_H2171_MED1_1_3904_lociStitched chr19 53829063 53833837 5_H2171_MED1_1_5224_lociStitched chr3 11299162 11324095 2_H2171_MED1_1_5986_lociStitched chr5 35395346 35406891 3_H2171_MED1_1_1693_lociStitched chr12 28296478 28309575 1_H2171_MED1_1_5922_lociStitched chr5 3542098 3546382 3_H2171_MED1_1_2604_lociStitched chr15 29544679 29560827 2_H2171_MED1_1_2254_lociStitched chr13 99297247 99306503 4_H2171_MED1_1_2041_lociStitched chr12 123445277 123474714 2_H2171_MED1_1_2141_lociStitched chr13 52466506 52478601 6_H2171_MED1_1_817_lociStitched chr1 230727775 230758255 3_H2171_MED1_1_2411_lociStitched chr14 73925775 73939983 1_H2171_MED1_1_6346_lociStitched chr6 15239481 15242062 2_H2171_MED1_1_31_lociStitched chr1 6252175 6261523 2_H2171_MED1_1_6334_lociStitched chr6 14651962 14658490 1_H2171_MED1_1_10_lociStitched chr1 1355263 1360155 1_H2171_MED1_1_534_lociStitched chr1 153237908 153244271 1_H2171_MED1_1_3988_lociStitched chr2 20600392 20605469 1_H2171_MED1_1_5909_lociStitched chr5 423764 428358 1_H2171_MED1_1_4170_lociStitched chr2 86115761 86118411 1_H2171_MED1_1_7411_lociStitched chr8 63579148 63586116 3_H2171_MED1_1_2624_lociStitched chr15 37633152 37638629 1_H2171_MED1_1_5911_lociStitched chr5 695232 697860 3_H2171_MED1_1_1253_lociStitched chr11 19713467 19724753 3_H2171_MED1_1_2541_lociStitched chr14 100247113 100254243 2_H2171_MED1_1_7301_lociStitched chr7 157275487 157282112 1_H2171_MED1_1_5103_lociStitched chr22 36214156 36218182 3_H2171_MED1_1_3372_lociStitched chr17 53332524 53350328 2_H2171_MED1_1_2657_lociStitched chr15 45586454 45593969 2_H2171_MED1_1_4694_lociStitched chr20 12456692 12465019 2_H2171_MED1_1_6684_lociStitched chr6 112571616 112582817 1_H2171_MED1_1_3996_lociStitched chr2 22829298 22831811 2_H2171_MED1_1_8040_lociStitched chr9 138704382 138711169 1_H2171_MED1_1_5920_lociStitched chr5 3445869 3449196 1_H2171_MED1_1_5760_lociStitched chr4 80303607 80306058

Example 3 Super-Enhancers in the Control of Cell Identity and Disease Introduction

Transcription factors bind DNA regulatory elements called enhancers, which play important roles in the control of cell type-specific gene expression programs (Bulger and Groudine, 2011; Calo and Wysocka, 2013; Carey, 1998; Lelli et al., 2012; Levine and Tjian, 2003; Maston et al., 2006; Ong and Corces, 2011; Panne, 2008; Spitz and Furlong, 2012; Xie and Ren, 2013). A typical mammalian cell contains thousands of active enhancers, and it has been estimated that there may be ˜1 million enhancers active in all human cells (Dunham et al., 2012; Heintzman et al., 2009; Thurman et al., 2012). It is important to further understand enhancers and their components because they control specific gene expression programs, and much disease-associated sequence variation occurs in these regulatory elements (Grossman et al., 2013; Hindorff et al., 2009; Lee and Young, 2013; Maurano et al., 2012).

The set of enhancers that control any one cell's gene expression program is probably best defined in murine embryonic stem cells (ESCs). Co-occupancy of murine ESC genomic sites by the master transcription factors Oct4, Sox2 and Nanog is highly predictive of enhancer activity (Chen et al., 2008), and 8,794 enhancers have been identified in ESCs by using ChIP-Seq datasets for Oct4, Sox2 and Nanog (Example 1; Whyte et al., 2013). A subset of these enhancers form 231 unusual enhancer domains at most genes that control the pluripotent state; these super-enhancers consist of clusters of enhancers that are densely occupied by five key ESC transcription factors and the Mediator coactivator (Example 1; Whyte et al., 2013). There are many additional transcription factors, cofactors and chromatin regulators that contribute to the control of ESCs (Ng and Surani, 2011; Orkin and Hochedlinger, 2011; Young, 2011), and it would be instructive to know how these occupy enhancers and super-enhancers in ESCs. Similarly, it would be useful to know if super-enhancers are transcribed, because enhancer RNAs (eRNAs) have been proposed to contribute to enhancer activity (Lai et al., 2013; Lam et al., 2013; Li et al., 2013; Ling et al., 2004; Mousavi et al., 2013; Orom et al., 2010).

Super-enhancers are associated with important genes that control cell state in cells where they have been identified thus far. In some embodiments, identification of these domains in additional cell types will provide a valuable resource for further study of cellular control. This example provides, among other things, a catalogue of super-enhancers in 86 human cell and tissue types. These super-enhancers are associated with genes encoding cell type-specific transcription factors, and thus identify candidate master transcription factors for many cell types. Using this catalogue, DNA sequence variation associated with specific diseases was found to be especially enriched in the super-enhancers of disease-relevant cells. Furthermore, tumor cells acquire super-enhancers at key oncogenes and at genes that function in the acquisition of hallmark capabilities in cancer, suggesting that these domains provide biomarkers for tumor-specific pathologies for diagnosis and therapeutic intervention.

Results Transcription Factors in ESCs

Super-enhancers are clusters of enhancers, formed by binding of high levels of master transcription factors and Mediator coactivator, that drive high level expression of genes encoding key regulators of cell identity (FIG. 3-1A) (Example 1; Whyte et al., 2013). Five ESC transcription factors were previously shown to occupy super-enhancers (Oct4, Sox2, Nanog, Klf4, and Esrrb) (Example 1; Whyte et al., 2013), but there are many additional transcription factors that contribute to the control of ESCs (Ng and Surani, 2011; Orkin and Hochedlinger, 2011; Young, 2011). We compiled ChIP-Seq data for 15 additional transcription factors in ESCs, for which high quality ChIP-Seq data was available, and investigated whether they occupy enhancers defined by Oct4, Sox2 and Nanog (OSN) co-occupancy (Example 1; Whyte et al., 2013) (Table 3-51). The analysis showed that six additional transcription factors (Nr5a2, Prdm14, Tcfcp211, Smad3, Stat3 and Tcf3) occupy both typical enhancers and super-enhancers, and that all of these are enriched in super-enhancers (FIG. 11(B)-(E)). Each of these factors has previously been shown to play important roles in ESC biology (Ng and Surani, 2011; Orkin and Hochedlinger, 2011; Young, 2011). In contrast, nine other transcription factors (c-Myc, CTCF, Zfx, Tbx3, YY1, Tfe3, Kapl/Zfp57, Smad1 and Ronin) were not similarly enriched in enhancers (Table 3-S1), and instead occupied other regions of the genome such as promoter-proximal sites or sites that border topological domains (FIG. 17A). It is particularly interesting that Smad3, Stat3 and Tcf3 are enriched in super-enhancer domains because these are transcription factor targets of the TGF-β, LIF and Wnt signaling pathways, respectively. Previous studies have shown that these transcription factors are recruited to enhancers formed by master transcription factors (Chen et al., 2008; Mullen et al., 2011), and evidence for enrichment of these factors at super-enhancers shows how these signaling pathways can converge on key genes that control ESC identity.

To assess whether the 11 transcription factors that are enriched at super-enhancers contribute to super-enhancer formation by binding to known DNA sequence motifs, we analyzed the frequency of these binding motifs at super-enhancer regions. For all nine transcription factors for which binding motifs are available, we found that the cognate motif showed significant enrichment at super-enhancer constituents relative to background expectation, and super-enhancers were enriched for these motifs compared to typical enhancers (FIG. 11F, FIG. 17B-C). These results suggest that the nine transcription factors contribute to super-enhancers by binding directly to their known DNA sequence motifs.

Previous studies have described a model of core transcriptional regulatory circuitry that includes Oct4, Sox2 and Nanog (Boyer et al., 2005). The evidence that these and additional ESC transcription factors form super-enhancers that drive genes essential for control of cell identity suggest a revised model of transcriptional regulatory circuitry for ESCs (FIG. 11G). This model contains an interconnected autoregulatory loop like that originally proposed for Oct4, Sox2 and Nanog (Boyer et al., 2005), but includes additional ESC transcription factors that meet three criteria: 1) their genes are driven by super-enhancers, 2) they co-occupy their own super-enhancers as well as those of the other master genes and 3) they play important roles in regulation of ESC state and iPSC reprogramming.

RNA Polymerase II, Co-Factors and Chromatin Regulators

Super-enhancers are occupied by unusually high levels of the Mediator coactivator (Example 1; Whyte et al., 2013). Previous studies have described the activities of RNA polymerase II and various cofactors, chromatin regulators and RNA at specific enhancers (Calo and Wysocka, 2013; Kagey et al., 2010; Lai et al., 2013; Lam et al., 2013; Li et al., 2013; Ling et al., 2004; Mousavi et al., 2013; Natoli and Andrau, 2012; Ong and Corces, 2011; Orom et al., 2010), so we used published and newly generated ChIP-Seq and RNA-Seq data to investigate how these components are associated with enhancers and super-enhancers across the ESC genome. The results indicate that RNA polymerase II, Mediator, cohesin, Nipb1, p300, CBP, Chd7, Brd4, and components of the esBAF (Brg1) and Lsd1-Nurd complexes are all enriched in super-enhancers relative to typical enhancers (FIG. 12A-E; Table 17). RNA polymerase II can transcribe enhancers, producing non-coding RNAs that in some cases contribute to enhancer activity (Kim et al., 2010; Lam et al., 2013; Li et al., 2013; Natoli and Andrau, 2012; Sigova et al., 2013); we found that RNA polymerase II and RNA were highly enriched at super-enhancers relative to typical enhancers (FIG. 12C).

It was notable that a broad spectrum of cofactors and chromatin regulators that are responsible for gene activation, enhancer looping, histone modification and nucleosome remodeling are especially enriched in ESC super-enhancers. The Mediator coactivator binds Nipb1, which loads cohesin, thus facilitating looping of enhancers to the promoters of their target genes (Kagey et al., 2010). The coactivator p300 is a histone acetyl-transferase, which is generally found at enhancer regions (Heintzman et al., 2007; Visel et al., 2009). CBP is a transcriptional co-activator that interacts with p300 and promotes synergy between enhancer components (Merika et al., 1998). Chd7 is a chromatin remodeler that also interacts with p300 and is often found at enhancers (Schnetz et al., 2010). Brd4, a member of the bromodomain protein family, binds to Mediator and acetylated histones, and is involved in regulation of transcriptional elongation by RNA polymerase II (Jang et al., 2005; Jiang et al., 1998). Brg1 is a subunit of the mammalian esBAF (SWI/SNF) complex, an ATP-dependent chromatin remodeler, which contributes to maintenance of pluripotency and self-renewal in ESCs (Ho et al., 2009a; Ho et al., 2009b). Lsd1, Hdac1, Hdac2, Mi-2b and Mbd3 are subunits of the Lsd1-Nurd complex, which possesses histone deacetylase, demethylase and nucleosome remodeling activities and contributes to enhancer decommissioning during differentiation (Denslow and Wade, 2007; Foster et al., 2010; Kaji et al., 2006; Kaji et al., 2007; Reynolds et al., 2012a; Reynolds et al., 2012b; Shi et al., 2004; Whyte et al., 2012).

Super-enhancers are occupied by an unusually large portion of the enhancer-associated RNA polymerase II and its associated cofactors and chromatin regulators. As measured by ChIP-Seq reads, between 12% and 36% of RNA polymerase II and the cofactors associated with all 8,794 enhancers were found within the 231 super-enhancers (FIG. 12C). The evidence that a large fraction of these enhancer cofactors are associated with super-enhancers helps explain why these large domains produce relatively high levels of RNA (FIG. 12C) and drive high-level expression of their associated genes when compared to typical enhancers (Example 1; Whyte et al., 2013). The presence of high levels of RNA at super-enhancers is especially interesting in light of recent studies suggesting that enhancer RNA contributes to gene activation (Lai et al., 2013; Lam et al., 2013; Li et al., 2013; Ling et al., 2004; Mousavi et al., 2013; Orom et al., 2010), and evidence that the MYOD1 super-enhancer is transcribed into eRNAs that contribute to the transcriptional activation of MYOD1 in muscle cells (Mousavi et al., 2013).

ESC differentiation causes preferential loss of expression of super-enhancer-associated genes, which may be a consequence of the unusual vulnerability of super-enhancers to perturbation of their components (Loven et al., 2013; Example 1; Whyte et al., 2013), (FIG. 18A-C). Without wishing to be bound by a particular theory, we speculate that this dual feature of super-enhancers—their ability to drive high level expression of key regulators of cell identity and their vulnerability to perturbation of their components—may facilitate cell state transitions during development.

Super-Enhancers in Many Cell Types

Because super-enhancers drive expression of genes that control and define cell identity, it would be useful to identify these elements and their associated genes in all human cells. However, the master transcription factors that might form super-enhancers are not known for most cell types and genome-wide binding data is limited for those that are known. We therefore explored the ability of various surrogate marks of enhancers (histone H3K27ac, H3K4me1, DNAse hypersensitivity, p300) to identify super-enhancers in ESCs (Creyghton et al., 2010; Heintzman et al., 2007; Neph et al., 2012; Rada-Iglesias et al., 2011; Shen et al., 2012; Visel et al., 2009). Of the marks available for a broad range of human samples, the histone H3K27ac modification was superior to the others in that it identified a large fraction of OSN-Mediator super-enhancers while minimizing excess sites (FIG. 19A).

We used H3K27ac ChIP-Seq data to create a catalogue of super-enhancers for 86 human cell and tissue samples (FIG. 13; Table 3-S2). A substantial portion of these super-enhancers and their associated genes are cell type-specific (FIG. 13A, FIG. 19B). In contrast, typical enhancer-associated genes are less cell type-specific (FIG. 19C). Characterization of super-enhancer-associated genes by Gene Ontology analysis revealed that they are linked to biological processes that largely define the identities of the respective cell and tissue types (FIG. 13B). Some of the super-enhancer domains overlap previously described locus control regions (LCRs), transcription initiation platforms (TIPs) and DNA methylation valleys (DMV) (FIG. 19D) (Bonifer, 2000; Forrester et al., 1990; Grosveld et al., 1987; Koch et al., 2011; Tuan et al., 1985; Xie and Ren, 2013).

To gain further understanding of the transcriptional regulatory circuitry of cells, and to facilitate efforts to reprogram cells for regenerative medicine, it would be valuable to identify the master transcription factors that control all cell states (Cherry and Daley, 2012; Graf and Enver, 2009; Lee and Young, 2013; Zhou et al., 2008). Super-enhancers were previously identified in 5 murine cell types (ESC, myotubes, pro-B cells, Th cells and macrophages), and the genes encoding known master transcription factors in these cells were found to have associated super-enhancers (Example 1; Whyte et al., 2013). We reasoned that candidate master transcription factors could be identified in most cells by identifying genes associated with super-enhancers that encode transcription factors and carried out this analysis in all the cells in this study. For those cells where master transcription factors have already been identified, this exercise captured the vast majority of these factors (FIG. 13C). A catalogue of candidate master transcription factors for other cell types can be found in Table 3-S3. In some embodiments, these candidates will be useful for deducing the transcriptional regulatory circuitry of a variety of different human cells and for reprogramming studies.

Disease-Associated DNA Sequence Variation in Super-Enhancers

Several recent studies suggest that much of disease-associated DNA sequence variation occurs in transcriptional regulatory regions defined by DNase hypersensitivity (Maurano et al., 2012; Vernot et al., 2012). We investigated the extent to which disease-associated DNA sequence variation occurs in enhancers and super-enhancers defined by histone H3K27ac. We compiled a list of 5,303 single nucleotide polymorphisms (SNP) linked to diverse phenotypic traits and diseases in 1,675 genome-wide association studies (GWAS), and investigated their distribution within enhancers and super-enhancers identified in the 86 human cell and tissue samples (FIG. 14A, Table 3-S4). We found that the majority of trait-associated SNPs occur in non-coding regions and that 64% of these occur within enhancer regions defined by H3K27ac (FIG. 14A). Thus 64% of trait-associated non-coding SNPs occur in the ˜33% of the genome covered by all enhancer regions defined by H3K27ac (Permutation test, P-value<10⁻⁴). The trait-associated SNPs were more enriched in super-enhancers than in typical enhancers (χ² test, P-value<10⁻¹²) (FIG. 20A), and for certain diseases, the enrichment in super-enhancers was particularly striking (FIG. 20B). These results confirm that much of disease-associated DNA sequence variation occurs in transcriptional regulatory regions of the genome, indicate that most of this variation occurs in enhancers, and reveal that variation disproportionately impacts super-enhancer domains.

If disease-associated SNPs occur disproportionately in super-enhancer domains, we would expect that SNPs associated with specific diseases would tend to occur in the super-enhancers of disease-relevant cells and not in those of disease-irrelevant cells. Indeed, for a broad spectrum of diseases, we found that disease-associated SNPs tend to occur in the super-enhancers of disease-relevant cells (FIG. 3-4B; Table 3-S4). This relationship was more pronounced for super-enhancers than typical enhancers (FIG. 20C). Since super-enhancers drive the expression of genes that control and define cell identity, these results suggest that altered expression of cell identity genes may often contribute to these diseases.

Examples of Disease-Associated SNPs in Super-Enhancers

We focused further study on several diseases where SNPs occur in super-enhancers of disease-relevant cell types in order to gain further insights into the relationship between these SNPs, specific super-enhancers and their associated genes. The diseases we selected for further study included Alzheimer's disease, type 1 diabetes, and systemic lupus erythematosus (FIG. 15).

Alzheimer's disease is a common form of dementia characterized by progressive neurodegeneration and loss of cognitive functions of the brain, and much of the genetic variation implicated in Alzheimer's disease is associated with amyloid precursor protein, transmembrane proteins and apolipoprotein E4 (Bertram and Tanzi, 2008; Tanzi, 2012). The SNP catalogue contains 27 SNPs linked to Alzheimer's disease and 5 of these occur in the super-enhancers of brain tissue (FIG. 15A). Thus, ˜19% (5/27) of all the Alzheimer's disease SNPs occur in the 1.4% of the genome encompassed by brain tissue super-enhancers (Permutation test, P-value<10⁻²). Two SNPs occur in the super-enhancer associated with the gene BIM (FIG. 15A), whose expression has recently been shown to be associated with Alzheimer's disease risk (Chapuis et al., 2013). Additional variation in the BIN1 super-enhancer, involving a small insertion, was shown to be associated with Alzheimer's disease (Chapuis et al., 2013).

Type 1 diabetes is caused by T-cell mediated autoimmune destruction of pancreatic beta cells, and much of the genetic variation implicated in type 1 diabetes is associated with major histocompatibility antigens, interleukin-2 signaling, T-cell receptor signaling and interferon signaling (Bluestone et al., 2010; Noble and Erlich, 2012). The SNP catalogue contains 76 SNPs linked to type 1 diabetes, and 67 of these occur in non-coding sequences. The non-coding SNPs were particularly enriched in the super-enhancers of primary Th cells, with 13 occurring in the super-enhancer regions of genes with prominent roles in Th cell biology (FIG. 15B). It was striking that 19% (13/67) of all the Type 1 diabetes SNPs in noncoding regions occur in the 1.3% of the genome encompassed by Th cell super-enhancers (Permutation test, P-value<10⁻⁴).

Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by the loss of tolerance for self-antigens and production of excess amounts of serum autoantibodies, and most genetic variation associated with SLE involves major histocompatibility antigens and lymphocyte signaling pathways (Costa-Reis and Sullivan, 2013; Deng and Tsao, 2010). The SNP catalogue contains 72 SNPs linked to SLE and 67 of these occur in non-coding regions. Among the cell types examined here, the non-coding SNPs occur most frequently in B cell super-enhancers, with 22 SNPs occurring in the super-enhancer regions of 16 genes that play key roles in B cell biology (FIG. 15C). Thus, 33% (22/67) of the SLE SNPs in non-coding regions occur in the 1.5% of the genome encompassed by B cell super-enhancers (Permutation test, P-value<10⁻⁴).

Similar enrichment of disease-associated variation in super-enhancers was observed for many additional diseases including rheumatoid arthritis, multiple sclerosis, systemic scleroderma, primary biliary cirrhosis, Crohn's disease, Graves disease, vitiligo and atrial fibrillation (Table 3-S4).

Super-Enhancers in Cancer

Super-enhancers associate with key oncogenes in several cancer cells (Loven et al., 2013). To gain further insights into the relationship between super-enhancers and cancer cell states, we used H3K27ac ChIP-Seq data to identify super-enhancers in 18 human cancer cells and identified their associated genes (Table 3-S2). The data revealed that a remarkable spectrum of known oncogene drivers have associated super-enhancers in this set of cancer cells (FIG. 16A; Table 3-S2). These results suggest that super-enhancers may be useful for identifying key oncogenes in specific cancers.

Further analysis of super-enhancers in tumor cells and related healthy cells suggests that cancer cells acquire super-enhancers at oncogene drivers during the process of tumor pathogenesis (FIG. 16B). For example, for multiple cancer cells, exceptionally large super-enhancers were found in the gene desert surrounding the c-MYC gene in the cancer cells but not in their healthy counterparts (FIG. 16B). Furthermore, the super-enhancers formed in the MYC locus were tumor type specific (FIG. 16B; FIG. 3-S5). These results are consistent with the model that cancer cells acquire cancer-specific super-enhancers at key oncogenes that are not present in their healthy counterparts.

DNA translocation, transcription factor overexpression and focal amplification occur frequently in cancer, and these mechanisms can account for the ability of cancer cells to acquire super-enhancers (FIG. 16C). In Multiple myeloma, for example, tumor cells often have a translocation that places the 3′ IgH super-enhancer adjacent the MYC gene (FIG. 16C). Overexpression of the TAL1 transcription factor in acute lymphoblastic leukemia (T-ALL) is associated with super-enhancer formation at another site in the MYC locus (FIG. 16C). And focal amplification in lung cancer involves a large super-enhancer that spans the MYC gene and its normal regulatory elements (FIG. 16C); tandem repeats of DNA segments can lead to the formation of clusters of enhancers.

Hanahan and Weinberg (2011) have proposed that cancer cells acquire a number of hallmark biological capabilities during the multistep process of tumor pathogenesis (Hanahan and Weinberg, 2011). We used these hallmarks as an organizing principle to investigate whether genes that acquire super-enhancers are associated with these biological capabilities in tumor cells. We identified super-enhancers that were acquired by cancer cells (not present in a healthy counterpart) and determined how their associated genes fit into the hallmarks. The results of such analysis with a colorectal cancer line revealed that over one-third of the super-enhancer genes have functions that are associated with a cancer hallmark (FIG. 16D-E; Table 3-S5). A similar analysis of two additional cancer lines confirmed that a large fraction of genes that acquire super-enhancers have hallmark functions (FIG. 16E, Table 3-S5). We conclude that cancer cells acquire cancer-specific super-enhancers at genes whose functions are associated with these hallmarks of cancer.

FIG. 11. Transcription Factors at Super-Enhancers

A) Distribution of Med1 ChIP-Seq signal at enhancers reveals two classes of enhancers in ESCs. Enhancer regions are plotted in an increasing order based on their input-normalized Med1 ChIP-Seq signal. Super-enhancers are defined as the population of enhancers above the inflection point of the curve. Example super-enhancers are highlighted along with their respective ranks and their associated genes. B) ChIP-Seq binding profiles for the indicated transcription factors at the POLE4 and miR-290-295 loci in ESCs. Red dots indicate the median enrichment of all bound regions in the respective ChIP-Seq datasets, and are positioned at maximum 20% of the axis height. (rpm/bp: reads per million per base pair) C) Metagene representations of the mean ChIP-Seq signal for the indicated transcription factors across typical enhancers and super-enhancer domains. Metagenes are centered on the enhancer region, and the length of the enhancer reflects the difference in median lengths (703 bp for typical enhancers, 8667 bp for super-enhancers). Additional 3 kb surrounding each enhancer region is also shown. D) Fold difference values of ChIP-Seq signal between typical enhancers and super-enhancers for the indicated transcription factors. Total signal indicates the mean ChIP-Seq signal (total reads) at typical enhancers and super-enhancers normalized to the mean value at typical enhancers. Density indicates the mean ChIP-Seq density at constituent enhancers (rpm/bp) of typical enhancers and super-enhancers normalized to the mean value at typical enhancers. Enhancer read % indicates the percentage of all reads mapped to enhancer regions that fall in the constituents of typical enhancer or super-enhancer regions. E) Metagene representations of the mean ChIP-Seq density for the indicated transcription factors across the constituent enhancers within typical enhancers and super-enhancers. Each metagene is centered on enhancer constituents. Additional 2.5 kb surrounding the constituent enhancer regions is also shown. F) Table depicting transcription factor binding motifs enriched at constituent enhancers within super-enhancer regions, and associated p-values. G) Revised model of the core transcriptional regulatory circuitry of ESCs. The model contains an interconnected autoregulatory loop consisting of transcription factors that meet three criteria: 1) their genes are driven by super-enhancers, 2) they co-occupy their own super-enhancers as well as those of the other transcription factor genes in the circuit, and 3) they play essential roles in regulation of ESC state and iPSC reprogramming. The layout of the circuit model was adapted from (Example 1; Whyte et al., 2013). See also FIG. 17, Table 3-51.

FIG. 12. RNA Polymerase II, Co-Factors and Chromatin Regulators at Super-Enhancers

A) ChIP-Seq binding profiles for RNA Polymerase II (RNAPII) and the indicated transcriptional co-factors and chromatin regulators at the POLE4 and miR-290-295 loci in ESCs. OSN denotes the merged ChIP-Seq binding profiles of the transcription factors Oct4, Sox2 and Nanog, and serves as a reference. Red dots indicate the median enrichment of all bound regions in the respective ChIP-Seq datasets, and are positioned at maximum 20% of the axis height. (rpm/bp: reads per million per base pair) B) Metagene representations of the mean ChIP-Seq signal for RNAPII and the indicated transcriptional co-factors and chromatin regulators across typical enhancers and super-enhancer domains. Metagenes are centered on the enhancer region, and the length of the enhancer reflects the difference in median lengths (703 bp for typical enhancers, 8667 bp for super-enhancers). Additional 3 kb surrounding each enhancer region is also shown. C) Fold difference values of ChIP-Seq signal between typical enhancers and super-enhancers for RNAPII and the indicated transcriptional co-factors and chromatin regulators, and RNA-Seq. Total signal indicates the mean ChIP-Seq signal (total reads) at typical enhancers and super-enhancers normalized to the mean value at typical enhancers. Density indicates the mean ChIP-Seq density at constituent enhancers (rpm/bp) of typical enhancers and super-enhancers normalized to the mean value at typical enhancers. Enhancer read % indicates the percentage of all reads mapped to enhancer regions that fall in the constituents of typical enhancer or super-enhancer regions. Reads mapped to exons were removed for the RNA-Seq analysis. D) Metagene representations of the mean ChIP-Seq density for RNAPII and the indicated transcriptional co-factors and chromatin regulators across the constituent enhancers within typical enhancers and super-enhancers. Each metagene is centered on enhancer constituents. Additional 2.5 kb surrounding the constituent enhancer regions is also shown. E) Model showing RNAPII, transcriptional co-factors and chromatin regulators that are found in ESC super-enhancers. The indicated proteins are responsible for diverse enhancer-related functions, such as enhancer looping, gene activation, nucleosome remodeling and histone modification. See also FIG. 18, Table 3-S1.

FIG. 13. Super-Enhancers and Candidate Master Transcription Factors in Many Cell Types

A) Heatmap showing the classification of super-enhancer domains across 26 human cell and tissue types. Color scale reflects the density of H3K27ac signal at the super-enhancer regions. B) Gene Ontology terms for super-enhancer-associated genes in 14 human cell and tissue types with corresponding p-values. C) Candidate master transcription factors identified in 6 cell types. All of these transcription factors were previously demonstrated to play key roles in the biology of the respective cell type or facilitate reprogramming to the respective cell type. See also FIG. 19, Table 3-S2, Table 3-S3.

FIG. 14. Disease-Associated DNA Sequence Variation in Super-Enhancers

A) Catalogue of single nucleotide polymorphisms (SNP) linked to phenotypic traits and diseases in genome wide association studies (GWAS). (left) Pie chart showing percentage of SNPs associated with the highlighted classes of traits and diseases. (middle) Distribution of trait-associated SNPs in coding and non-coding regions of the genome. (right) Location of all non-coding trait-associated SNPs relative to all enhancers identified in 86 human cell and tissue samples. X-axis reflects binned distances of each SNP to the nearest enhancer. SNPs located within enhancers are assigned to the 0 bin. B) Radar plots showing the density of trait-associated non-coding SNPs linked to the highlighted traits and diseases, in the super-enhancer domains identified in 12 human cell and tissue types. The center of the plot is 0, and a colored dot on the respective axis indicates the SNP density (SNP/10 MB sequence) in the super-enhancer domains of each cell and tissue type. Lines connecting the density values to the origin of the plot are added to improve visualization. See also FIG. 10, Table 3-S2, Table 3-S4.

FIG. 15. Examples of Disease-Associated SNPs in Super-Enhancers

A) (top left) Radar plots showing the density of non-coding SNPs linked to Alzheimer's disease (AD) in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types. The center of the plot is 0, and a colored dot on the respective axis indicates the SNP density (SNP/10 MB sequence) in the super-enhancer domains or typical enhancers of each cell and tissue type. Lines connecting the density values to the origin of the plot are added to improve visualization. (top right) Distribution of non-coding SNPs linked to AD in the typical enhancers and super-enhancers of brain tissue. (bottom left) List of genes associated with AD SNP-containing super-enhancers in brain tissue. (bottom right) ChIP-Seq binding profile for H3K27ac at the BIN1 locus in brain tissue. The positions of AD-SNPs are highlighted as red bars, and the super-enhancers are highlighted as black bars above the binding profile. Indel rs59335482 (a three base pair insertion) is also highlighted. (rpm/bp: reads per million per base pair) B) (top left) Radar plots showing the density of non-coding SNPs linked to type 1 diabetes (T1D) in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types. The center of the plot is 0, and a colored dot on the respective axis indicates the SNP density (SNP/10 MB sequence) in the super-enhancer domains or typical enhancers of each cell and tissue type. Lines connecting the density values to the origin of the plot are added to improve visualization. (top right) Distribution of non-coding SNPs linked to T1D in the typical enhancers and super-enhancers of Th cells. (bottom left) List of genes associated with T1D SNP-containing super-enhancers in Th cells. (bottom right) ChIP-Seq binding profile for H3K27ac at the IL2RA locus in Th cells. The positions of T1D SNPs are highlighted as red bars, and the super-enhancers are highlighted as black bars above the binding profile. C) (top left) Radar plots showing the density of non-coding SNPs linked to systemic lupus erythematosus (SLE) in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types. The center of the plot is 0, and a colored dot on the respective axis indicates the SNP density (SNP/10 MB sequence) in the super-enhancer domains or typical enhancers of each cell and tissue type. Lines connecting the density values to the origin of the plot are added to improve visualization. (top right) Distribution of non-coding SNPs linked to SLE in the typical enhancers and super-enhancers of B cells. (bottom left) List of genes associated with SLE SNP-containing super-enhancers in B cells. (bottom right) ChIP-Seq binding profile for H3K27ac at the HLA-DRB1 and HLA-DQA1 loci in B cells. The positions of SLE SNPs are highlighted as red bars, and the super-enhancers are highlighted as black bars above the binding profile. See also Table 3-S2, Table 3-S4.

FIG. 16. Super-Enhancers in Cancer

A) Selected genes associated with super-enhancers in the indicated cancers. Blue box indicates the gene being associated with a super-enhancer in the respective cancer. CML stands for chronic myelogenous leukemia. B) Cancer cells acquire super-enhancers. ChIP-Seq binding profiles for H3K27ac are shown at the gene desert surrounding MYC in pancreatic cancer, T cell leukemia, colorectal cancer, and healthy counterparts. In colorectal cancer several regions in the 1 MB window upstream of MYC were shown to interact with the MYC gene in colorectal cancer (Ahmadiyeh et al., 2010; Pomerantz et al., 2009). (rpm/bp: reads per million per base pair) C) Chromosomal translocation, overexpression of transcription factors and focal amplification may contribute to super-enhancer formation in cancer. Displayed are ChIP-Seq binding profiles for H3K27ac and indicated transcription factors at the gene desert surrounding MYC in the indicated cancers. (top) A translocation event places the MYC gene proximal to an inserted IgH super-enhancer in multiple myeloma. (middle) Tall binding is observed at a distal super-enhancer in T cell leukemia. (bottom) Large H3K27ac domains are observed at the site of focal amplification in lung cancer. The red bars below the binding profiles indicate the genomic positions of focal amplification in six different samples, two of which (SM09-019T and SM09-11T1) are primary patient samples (Iwakawa et al., 2013). D) Tumor-specific super-enhancers associate with hallmark cancer genes in colorectal cancer. (top) Diagram of the ten hallmarks of cancer adapted from Hanahan and Weinberg, 2011. Genes associated with super-enhancers in colorectal cancer but not in healthy colon samples were assigned to hallmark categories based on their functions and their previous implication in tumorigenesis. Prominent genes that associate with tumor-specific super-enhancers are highlighted at each cancer hallmark. (bottom) Distribution of H3K27ac signal across enhancers identified in colorectal cancer. Uneven distribution of signal allows the identification of 387 super-enhancers. Prominent genes associated with super-enhancers in colorectal cancer but not in healthy colon are highlighted with their respective super-enhancer ranks and cancer hallmarks they were assigned to. E) Super-enhancers acquired by cancer cells associate with hallmark genes. Each cancer hallmark was assigned a Gene Ontology term, and the number of genes that are associated with acquired super-enhancers and are included in that GO term is displayed for each cancer. Asterisk denotes statistical significance above genomic expectation (hypergeometric test, p<0.05). See also FIG. 3-21, Table 3-S2, Table 3-S5. FIG. 17. Genomic Localization and Features of Transcription Factors in mESCs. Related to FIG. 11. (A) Metagene representations of mean ChIP-Seq density in regions surrounding constituents of super-enhancers and typical enhancers, active promoters, and the borders of topological domains for the indicated transcription factors in mESCs. For each transcription factor, the leftmost panel shows background-subtracted densities within size-normalized constituents of super-enhancers (red) and typical enhancers (grey) plus adjacent 2.5 kb regions. The center panel shows background-subtracted densities within 1 kb of RefSeq-defined transcription start sites of active transcripts. Active transcripts were defined as having an RNA Polymerase II mean ChIP-Seq signal >1 rpm/bp in this region. The right panel shows background-subtracted densities within +/−500 kb of borders of topological domains in mESC as defined in (Dixon et al., 2012). (B) (top) Table depicting transcription factor binding motifs at constituent enhancers within typical enhancer regions, and associated p-values. P-values for motifs within typical enhancers arise by comparison of 1573 typical enhancer constituents to genomic background (see Extended Experimental Procedures). Many typical enhancer p-values thus appear more significant than their counterparts at super-enhancers (FIG. 11F), but the P-values are not directly comparable due to the difference in sample size between the two classes of enhancers. C) Comparison of motif frequency per constituent of super-enhancers and typical enhancers shows that super-enhancer constituents are enriched in motif occurrences for these factors compared to typical enhancer constituents (t test, p<10⁻¹⁵). Box plot whiskers extend to 1.5× the interquartile range. FIG. 18. Super-Enhancer-Associated Genes are Especially Sensitive to Perturbation. Related to FIG. 12. (A) (top) Schematic diagram the shRNAs knockdown of Oct4 in mESCs. (bottom) Box plots of fold change expression for all enhancer-associated genes, typical enhancer-associated genes and super-enhancer-associated genes 3, 4 and 5 days after knockdown. Expression values were normalized to the values measured in ESCs transduced with a control shRNA against GFP. Box plot whiskers extend to 1.5× the interquartile range. (B) (top) Schematic diagram the shRNAs knockdown of the Mediator subunit Med12 in mESCs. (bottom) Box plots of fold change expression for all enhancer-associated genes, typical enhancer-associated genes and super-enhancer-associated genes 3, 4 and 5 days after knockdown. Expression values were normalized to the values measured in ESCs transduced with a control shRNA against GFP. Box plot whiskers extend to 1.5× the interquartile range. (C) (top) Schematic diagram the shRNAs knockdown of the cohesin subunit Smc1 in mESCs. (bottom) Box plots of fold change expression for all enhancer-associated genes, typical enhancer-associated genes and super-enhancer-associated genes 3, 4 and 5 days after knockdown. Expression values were normalized to the values measured in ESCs transduced with a control shRNA against GFP. Box plot whiskers extend to 1.5× the interquartile range. FIG. 19. Identification and Characterization of Super-Enhancers Using H3K27Ac. Related to FIG. 13. (A) Comparison of the abilities of enhancer surrogate marks (p300, H3K27ac, H3K4me1, DNase hypersensitivity) to identify super-enhancers and super-enhancer-associated genes in mESCs. (top) ChIP-Seq binding profiles for OSN (merged binding profiles of the transcription factors Oct4, Sox2 and Nanog), Mediator (Med1), p300, H3K27ac, H3K4me1 and DNase hypersensitivity at the POLE and miR-290-295 loci in mESCs. Red dots indicate the median enrichment of all bound regions in the respective ChIP-Seq datasets, and are positioned at maximum 20% of the axis height. (rpm/bp: reads per million per base pair) (middle left) Venn diagrams showing the overlap between super-enhancer domains identified by Oct4, Sox2, Nanog and Med1 data versus those identified using p300, H3K27ac, H3K4me1 ChIP-Seq data or DNase hypersensitivity data. (middle right) Venn diagrams showing the overlap between super-enhancer-associated genes identified by Oct4, Sox2, Nanog and Med1 data versus those identified by p300, H3K27ac or H3K4me1, ChIP-Seq data or DNase hypersensitivity data. We note that even though p300 appears to be an excellent enhancer surrogate to identify super-enhancers, p300 ChIP-Seq data for a large set of human samples are as yet not available. Super-enhancers identified by H3K27ac but not by OSN-Mediator are characterized by low Mediator ChIP-Seq signal, and associate with genes linked to ubiquitous biological processes such as transcription, indicating that OSN-Med1-identified super-enhancers are a subset of the super-enhancers identified by H3K27ac, and suggesting that transcription factors other than cell type specific master transcription factors may form large domains in the genome. (bottom, heatmap) Heatmap representation of H3K27ac and Med1 ChIP-Seq densities at the 392 super-enhancer regions identified by H3K27ac in mESC. Super-enhancer regions are shown along with 5 kb flanking distance up- and downstream. Color scale reflects the density of H3K27ac signal at the super-enhancer regions. (bottom, GO analysis) Gene Ontology analysis the indicated gene sets. B) Heatmap showing the classification of super-enhancer-associated genes across 26 human cell and tissue types. Each row is a gene and red color indicates the gene being associated with a super-enhancer in the respective cell type. C) Heatmap showing the classification of typical enhancer-associated genes across 26 human cell and tissue types. Each row is a gene and red color indicates the gene being associated with a super-enhancer in the respective cell type. D) Super-enhancers can overlap with Locus Control Regions (LCR), Transcription Initiation Platforms (TIP) and DNA methylation valleys (DMV). FIG. 20. Disease-Associated Sequence Variation is Enriched in Super-Enhancers. Related to FIG. 14. (A) Summary of trait-associated SNPs in the union of super-enhancers, typical enhancers and regulatory regions (defined as H3K27ac binding peaks) in 86 human cell and tissue samples. Displayed is the percentage of the total 4,378 trait-associated non-coding SNPs falling into these regions. The percentage of the genome (3.4 billion bases) covered by the union of these regions in the 86 human cell and tissue types is also displayed. SNP enrichment is defined as the percent of SNPs contained in the percent of the genome covered for these regions. B) The SNP enrichment values of non-coding SNPs linked to the highlighted traits and diseases in the union of super-enhancers, typical enhancers and regulatory regions (defined as H3K27ac binding peaks) in 86 human cell and tissue samples. C) Radar plots showing the density of non-coding SNPs linked to selected diseases in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types. The center of the plot is 0, and a colored dot on the respective axis indicates the SNP density (SNP/10 MB sequence) in the super-enhancer domains or typical enhancers of each cell and tissue type. Lines connecting the density values to the origin of the plot are added to improve visualization. FIG. 21. Super-Enhancers Around the MYC Locus. Related to FIG. 16. ChIP-Seq binding profiles for H3K27ac at the c-MYC locus in the indicated cancer samples. Super-enhancers are highlighted as black bars above the binding profile. Purple track indicates the topological domains identified in hESC in (Dixon et al., 2012). (rpm/bp: reads per million per base pair)

Super-enhancers, typical enhancers and their associated genes in 86 human cell and tissue samples (Related to FIG. 13, FIG. 14, FIG. 15, FIG. 16, FIG. 19, FIG. 20, FIG. 21) are show in the Appendix to the subject application. The Appendix containing 86 tables (i.e., Tables 5-90), each containing stitched enhancers, associated genes, and ChIP-Seq signal. Columns are: enhancer ID, chromosome, start, end, associated gene, enhancer rank, is enhancer a super-enhancer (1:yes, 0:no), H3K27ac ChIP-Seq density (rpm/bp), read density in corresponding input sample (rpm/bp), the entire contents of which is incorporated by reference.

Discussion

Super-enhancers were previously identified in a small number of cells, where they were shown to consist of large clusters of transcriptional enhancers formed by binding of master transcription factors and to be associated with genes that control and define cell identity (Loven et al., 2013; Example 1; Whyte et al., 2013). We have extended our understanding of super-enhancers by identifying the population of transcription factors, cofactors, chromatin regulators and core transcription apparatus that occupy these domains in embryonic stem cells and by demonstrating that super-enhancers are highly transcribed. We have created a catalogue of super-enhancers for 86 different human cell and tissue types and shown that these are associated with genes encoding cell type-specific transcription factors and other components that play important roles in cell type-specific biology. Interestingly, we find that sequence variation associated with a broad spectrum of diseases is especially enriched in the super-enhancers of disease-relevant cell types and that cancer cells generally acquire super-enhancers at oncogenes and other genes that play important roles in cancer pathogenesis.

The enhancers and transcription factors that control embryonic stem cell state are probably better understood than those for any other cell type, making ESCs an excellent model for identifying components of super-enhancers (Ng and Surani, 2011; Orkin and Hochedlinger, 2011; Young, 2011). Several important insights were gained by studying how >35 transcription factors, cofactors, chromatin regulators and components of the core transcription apparatus occupy enhancers and super-enhancers in ESCs. All the enhancer-binding transcription factors are enriched at super-enhancers, with some so highly enriched that they distinguish super-enhancers from typical enhancers. The transcription factor targets of the TGF-β, LIF and Wnt signaling pathways are enriched in super-enhancers, suggesting how these signaling pathways converge on key genes that control ESC identify. Super-enhancers are occupied by a large portion of the enhancer-associated RNA polymerase II and its associated cofactors and chromatin regulators, which can explain how they contribute to high-level transcription of associated genes. Furthermore, the levels of RNA detected at super-enhancers vastly exceed those at typical enhancers, and recent evidence suggests that these eRNAs may contribute to gene activation (Lai et al., 2013; Lam et al., 2013; Li et al., 2013; Ling et al., 2004; Mousavi et al., 2013; Orom et al., 2010).

We have generated a catalogue of super-enhancers and their associated genes in a broad spectrum of human cell and tissue types. The super-enhancers tend to be cell type-specific and the genes associated with these elements tend to be cell type-specific in their expression and linked to biological processes that largely define the identities of the respective cell and tissue types. Genes that encode candidate master transcription factors and non-coding RNAs such as miRNAs are among those associated with super-enhancers. Thus, in some embodiments, the super-enhancer catalogue provides a valuable resource for further study of transcriptional control of cell identity and for reprogramming (Cherry and Daley, 2012; Graf and Enver, 2009; Lee and Young, 2013; Zhou et al., 2008).

Several recent studies suggest that much of disease-associated DNA sequence variation occurs in transcriptional regulatory regions defined by DNase hypersensitivity (Maurano et al., 2012; Vernot et al., 2012). We found that disease-associated SNPs occur in super-enhancers of disease-relevant cells and that this occurs more frequently for super-enhancers than typical enhancers. Since super-enhancers drive the expression of genes that control and define cell identity, these results suggest that altered expression of cell identity genes may often contribute to these diseases. In some embodiments, hypotheses regarding the role of specific cell types and genes in many diseases might be guided in the future by knowledge of super-enhancers.

Cancer cells acquire super-enhancers at oncogene drivers during the process of tumor pathogenesis. Cancer cells appear to acquire super-enhancers through a variety of mechanisms, including chromosomal translocation of super-enhancers normally associated with other genes, focal amplification, or overexpression of an oncogenic transcription factor. The super-enhancers acquired by cancer cells are associated with a remarkably broad spectrum of oncogenes that have been described thus far in cancer (Bishop, 1987; Fearon and Vogelstein, 1990; Forbes et al., 2010; Futreal et al., 2004; Garraway and Lander, 2013; Hanahan and Weinberg, 2011; Vogelstein et al., 2013). They are also associated with genes that function in the acquisition of hallmark capabilities in cancer (Hanahan and Weinberg, 2011). Thus, in some embodiments, super-enhancers provide biomarkers for cancer-specific pathologies valuable for further understanding cancer biology, diagnosis and therapy.

Methods Data Analysis

ChIP-Seq datasets were aligned using Bowtie (version 0.12.9) to build version mm9 of the mouse genome or build version hg19 of the human genome. The GEO accession IDs for all analyzed datasets are listed in Table 3-S 6.

Normalized read density of a ChIP-Seq dataset in any region was calculated as described (Example 1; Whyte et al., 2013). ChIP-Seq reads aligning to the region were extended by 200 bp and the density of reads per base pair (bp) was calculated. The density of reads in each region was normalized to the total number of million mapped reads producing read density in units of reads per million mapped reads per base pair (rpm/bp).

MACS version 1.4.1 (Model based analysis of ChIP-Seq) (Zhang et al., 2008) peak finding algorithm was used to identify regions of ChIP-Seq enrichment over background. A p-value threshold of enrichment of 1e-9 was used for all datasets.

Enhancers were defined as regions of ChIP-Seq enrichment for transcription factors in murine ESCs, and H3K27ac in human cells. To accurately capture dense clusters of enhancers, enhancer regions within 12.5 kb of one another were allowed to be stitched together.

ChIP-Seq

ChIP-Seq for Ronin was previously described (Dejosez et al., 2010). ChIP-Seq for Mbd3 in the murine ESC line V6.5 was performed with an anti-Mbd3 antibody (Santa Cruz, SC-9402) as described (Whyte et al., 2012). ChIP-Seq for CBP in the murine ESC line V6.5 was performed with an anti-CBP antibody (Santa Cruz, SC-9402) as described (Mullen et al., 2011). ChIP-Seq for H3K27ac in RPMI-8402 cells was performed with an anti-H3K27ac antibody (Abcam, ab4729) as described (Sanda et al., 2012).

Several as yet unreleased ChIP-Seq datasets were generously shared by the NIH Roadmap Epigenome project (Bernstein et al., 2010).

ChIP-Seq Density Analysis

ChIP-Seq read density was measured as described in (Lin et al., 2012). Briefly, ChIP-Seq reads were extended 200 bp and the density of reads per base pair was calculated. This density was normalized to the millions of mapped reads contributing to the density, measured in reads per million per base pair (rpm/bp).

Percent enhancer signal falling in super-enhancers (FIGS. 1D and 2C) was calculated using the sum of signal (density*length) of super-enhancers and typical enhancers. Comparison of super-enhancer vs. typical enhancer signal was calculated using mean background-subtracted signal (density*length) of super-enhancers divided by the sum of super-enhancers and typical enhancers.

Enhancers and Super-Enhancers in mESC

Genomic coordinates of murine embryonic stem cell typical enhancers, super-enhancers, typical enhancer constituents and super-enhancer constituents were downloaded from (Whyte et al., 2013).

Threshold for Occupancy at Enhancers

For FIGS. 1 and 2, the occupancy of transcription factors, co-factors and chromatin regulators at enhancers in ESCs was determined as follows. The mean ChIP-Seq density at every enhancer constituent was calculated for each transcription factor, co-factor and chromatin regulator listed in Table 3-S 1. Mean ChIP-Seq density values measured in the corresponding input samples were subtracted. To correct for ChIP-Seq background signal, a minimum value of 0.2 rpm/bp after background subtraction was required for further consideration. To correct for different ChIP-Seq qualities across multiple samples, the mean ChIP-Seq densities of random genomic regions of equivalent sizes of the enhancer constituents were calculated (Table 3-S 1), and the ratio of the mean ChIP-seq signal at enhancer constituents and the mean ChIP-seq signal at the random genomic positions was calculated. Presence of a factor at enhancers was defined as this ratio >9. We found that these two thresholds largely captured the definition of presence or absence at enhancers for several factors where genomic localization of the factor has previously been analyzed in a similar context.

USCS Browser Tracks

To assess the relative enrichment of binding peaks compared to other peaks in ChIP-Seq samples displayed as UCSC Browser tracks (FIG. 11(B), FIG. 12(A), FIG. 19(A) the median enrichment value for all bound regions was calculated. MACS was used to identify enriched regions (as described below), and the background subtracted read density at the enriched regions was determined. The median read density value of all enriched regions is denoted by a red dot on the y-axis of the UCSC Browser tracks.

FIG. 16(C) (top), depicts a described translocation event that between chr8(q24) and chr3(q21) in the multiple myeloma cell line MM1S (Shou et al., 2000). The segment of chromosomal region chr3(q21) depicted on the figure is chr3:122,500,000-124,250,000.

The sites of focal amplification FIG. 16(C) (bottom) in small cell lung cancer were described in (Iwakawa et al., 2013).

Overlaps with Large Genomic Regions

The genomic co-ordinates for the DNA-methylation valleys were obtained from (Xie and Ren, 2013). The cell types pooled on FIG. 19(D) include, hESC, mesenchymal stem cell, mesendoderm, neural progenitor and trophoblast (DMV), and hESC, fetal intestine, fetal large intestine, fetal thymus, fetal hematopoietic progenitor and fetal muscle (SE).

The genomic co-ordinates for the globin LCR and TIP at the IFNAR1 loci were adapted from (Bonifer, 2000; Koch et al., 2011)

Metagenes and Heatmaps

Genome-wide average “meta” representations of ChIP-Seq density at typical enhancers and super-enhancers (FIG. 11(C), 12(B)) were created by mapping reads to the enhancer regions and flanking regions. Each enhancer or flanking region was split into 100 equally sized bins. This split all enhancer regions, regardless of their size, into 300 bins. All typical enhancer or super-enhancer regions were then aligned and the average ChIP-seq density in each bin was calculated to create a meta genome-wide average in units of reads per million per base pair. In order to visualize the length disparity between typical and super-enhancer regions, the enhancer region (between its actual start and end) was scaled relative to its median length.

Constituent metagenes (FIG. 11(E), 12(D), FIG. 17(A) were created in a similar fashion. Constituents of super- and typical enhancers, as well as 2.5 kb upstream and downstream were each broken into 50 bins. The ChIP-Seq density in these regions was calculated in and combined together to get 150 bins spanning 2.5 kb upstream, the constituent enhancer, and 2.5 kb downstream. The average combined profiles for the super- or typical enhancers constituents is shown.

Metagenes around expressed promoters were similarly created. Promoters were defined as +/−1 kb around the TSS. 9,667 expressed promoters were defined as those having RNAPII ChIP-Seq density >1 rpm/bp. The regions were broken into 50 bins and the average read density for expressed promoters is shown (FIG. 17(A)).

Metagenes around boundaries of topological domains (TD) were similarly created. Topological domains defined in (Dixon et al., 2012) were downloaded for the mm9 genome build. Regions interrogated were +/−500 kb from the TD border and were split into 100 bins. The average read density per bin is shown (FIG. 17(A)).

Heatmaps in FIG. 13(A) and FIG. 19(A) were calculated in a manner similar to metagenes. The union of 26 sets of representative super-enhancers resulted in 5,988 regions used for H3K27ac density analysis in FIG. 13(A). Each element in the union was broken into 50 equally sized bins. Reads were extended 200 bp and reads-per-million densities were calculated in each element in the union of super-enhancers. FIG. 19(A) contains a heatmap showing densities in H3K27ac-defined super-enhancers. Regions 5 kb upstream and downstream of the super-enhancers are shown. Each region (upstream, super-enhancer, downstream) is broken into 50 equally sized bins. Reads were extended 200 bp and reads-per-million normalized densities were calculated in these regions.

Motif Analysis

To find sequence motifs enriched in super-enhancers in murine ESCs, we analyzed the genomic sequence under the constituents within super-enhancers. We extracted their sequence from the mm9 genome and used this as input for TRAP using TRANSFAC vertebrates as the comparison library, mouse promoters as the control, and Benjamini-Hochberg as the correction (Thomas-Chollier et al., 2011). To include Tcfcp211, we used the Jaspar vertebrates as the comparison library. P-values displayed in FIG. 11(F) correspond to the corrected P in the output. Motif enrichment analysis at typical enhancers (FIG. 17(B)) was done the same way, but only the enhancer constituents with a size smaller than 500 bp were used, because of limitations of TRAP. P-values displayed in FIG. 17(B) correspond to the corrected P in the output.

For the boxplot displayed on FIG. 17(C), the sum of the number of motifs was counted in each super-enhancer constituent and typical enhancer constituent, and this analysis did not include the Tcfcp211 motif. For this analysis, we used FIMO with a custom library of all TRANSFAC motifs at a p-value threshold of 10⁻⁴ (Grant et al., 2011; Matys et al., 2006). The number of occurrences of each motif was summed for each region and enrichment differences were calculated using a two-tailed t test.

Matrices used: Oct4: M01124; Sox2: M01272; Nanog: M01123; Klf4: M01588; Esrrb: M01589; Stat3: M01595; Tcf3: M01594; Smad3: M00701; Tcfcp211: MA0145.

The motif logos displayed on FIG. 11(F) and FIG. 17(B) were downloaded from the Cistrome database (Liu et al., 2011).

Identifying ChIP-Seq Enriched Regions in Human Cells

Human sequencing reads were aligned to the human genome build hg19 (GRCh37) using bowtie 0.12.9 (Langmead et al., 2009) using parameters -k 2, -m 2, -n 2, --best. Mouse sequencing reads were aligned to the mouse genome build mm9 (NCBI37) using bowtie 0.12.9 using parameters -k 1, -m 1, -n 2, --best. Regions of enrichment of H3K27ac in human samples were calculated using MACS 1.4.2 (Zhang et al., 2008) using parameters -p 1e-9, --keep-dup=auto, -w -S -space=50, and -g hs on H3K27ac ChIP-Seq with control libraries. MACS peaks were called on mouse ChIP-Seq using -p 1e-9, --keep-dup=auto, -w -S -space=50, -g mm. UCSC Genome Browser (Kent et al., 2002) tracks were generated using MACS wiggle outputs. MACS peaks of human H3K27ac were used as constituent enhancers for super-enhancer identification.

Enhancers and Super-Enhancers in Human Cells

Enhancers were stitched and super-enhancers were identified using ROSE (https://bitbucket.org/young_computation/rose), which is an implementation of the algorithm described in (Loven et al., 2013). Briefly, this algorithm stitches constituent enhancers together if they are within a certain distance and ranks the enhancers by their input-subtracted signal of H3K27ac. It then separates super-enhancers from typical enhancers by identifying an inflection point of H3K27ac signal vs. enhancer rank (Example 1; Whyte et al., 2013). ROSE was run with a stitching distance of 12,500 bp, i.e. we allowed enhancers within 12,500 bp to be stitched together. In addition, we used a promoter exclusion zone of 2,000 bp, i.e. if a constituent enhancer was wholly contained within a window +/−1,000 bp around an annotated transcription start site, the constituent enhancer was excluded from stitching.

Stitched enhancers were assigned to the expressed transcript whose TSS was the nearest to the center of the stitched enhancer. Expressed transcripts were defined as having an at least 0.5 mean rpm/bp H3K27ac ChIP-Seq density in a window 500 bases up- and downstream of the TSS. In cases where enhancer-gene assignments were previously verified by experimental techniques, we assigned genes based on those studies. These examples include: MYC in multiple myeloma, IRF4 in multiple myeloma (Loven et al., 2013), MYC in colorectal cancer, breast cancer and prostate cancer (Ahmadiyeh et al., 2010; Pomerantz et al., 2009) (all on FIG. 3-6).

For the FIG. 13(A) heatmap, the union of super-enhancers for 26 cell types was taken. The rpm/bp density of ChIP-Seq reads (extended by 200 bp) was calculated for the corresponding 26 H3K27ac datasets and is represented by color intensity. Each region in the union of super-enhancers was compared to every super-enhancer in the 26 cell types, and the cell types containing a super-enhancer that contacts a region in the union were recorded. The heatmap is sorted first by the number of cell types containing a contacting super-enhancer and then by the order of cell types containing a contacting super-enhancer.

Gene Sets and Annotations

All analyses were performed using RefSeq (GRCh37/hg19) human gene annotations or RefSeq (NCBI37/mm9) mouse gene annotations (Pruitt et al., 2007).

The high confidence set of transcription factors used for analysis was the intersection of genes identified as transcription factors in two different transcription factor databases (AnimalTFDB and TcoF) (Schaefer et al., 2011; Zhang et al., 2012).

References for the Validation of Candidate Master Transcription Factors

The references validating the transcription factors listed on FIG. 3-3C, as candidate master transcription factors are as follows:

Brain: NKX2-2 (Briscoe et al., 1999; Panman et al., 2011), OLIG1 (Arnett et al., 2004), BRN2 (Ambasudhan et al., 2011; McEvilly et al., 2002; Pfisterer et al., 2011; Son et al., 2011; Sugitani et al., 2002), SOX10 (Bondurand and Sham, 2013; Britsch et al., 2001; Lee et al., 2008), SOX2 (Bergsland et al., 2011; Cavallaro et al., 2008; Ferri et al., 2004; Han et al., 2012; Ring et al., 2012).

Heart: TBX20 (Cai et al., 2005; Cai et al., 2013; Takeuchi et al., 2005), TBX5 (Ieda et al., 2010; Nadeau et al., 2010; Qian et al., 2012; Song et al., 2012), MEF2A (Naya et al., 2002; Schlesinger et al., 2011), NKX2-5 (Lyons et al., 1995; Schlesinger et al., 2011), GATA4 (Ieda et al., 2010; Nadeau et al., 2010; Qian et al., 2012; Song et al., 2012; Turbendian et al., 2013; Watt et al., 2004).

Skeletal muscle: MYOD1 (Bergstrom et al., 2002; Davis et al., 1987; Rudnicki et al., 1993; Tajbakhsh et al., 1997), PITX2 (Gherzi et al., 2010; Lin et al., 1999), SIX1 (Grifone et al., 2004; Yajima et al., 2010), TEAD4 (Benhaddou et al., 2012).

Lung: NFIB (Hsu et al., 2011), TBX5 (Arora et al., 2012), CEBPA (Martis et al., 2006), TBX2 (Ludtke et al., 2013), TBX3 (Ludtke et al., 2013).

Adipose tissue: PPARG (Lehrke and Lazar, 2005; Rosen et al., 1999; Rosen et al., 2000; Schupp et al., 2009), CEBPB (Cao et al., 1991; Kajimura et al., 2009), CEBPD (Rosen et al., 2000; Tanaka et al., 1997), CREB1 (Reusch et al., 2000).

B cell: IKZF3 (Ferreiros-Vidal et al., 2013; Kioussis, 2007; Ma et al., 2010), PAX5 (Busslinger, 2004; Medvedovic et al., 2011), BACH2 (Kallies and Nutt, 2010), OCT2 (Gstaiger et al., 1996; Wirth et al., 1995), IKZF1 (Ferreiros-Vidal et al., 2013; Kioussis, 2007; Ma et al., 2010), IRF8 (Busslinger, 2004).

Gene Ontology (GO) Analysis

For gene ontology analysis, a subset of 26 datasets, representing the diversity of tissues in the collection used for this study, were first selected. For each tissue, the genes that were associated with super-enhancers in that tissue and no more than two other tissues in the subset were analyzed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp). For each tissue, the three top scoring categories (ie the categories with the lowest p-values) were selected for display. A threshold p-value score of 2E-05 was incorporated as a minimum requirement filter for scoring as a top category.

Trait-Associated SNPs

Trait-associated SNPs were downloaded from the NHGRI database of genome-wide association studies on Aug. 9, 2013, which contained 13,957 entries/rows. Since SNPs more strongly associated with a trait are suggested to have a higher likelihood of being causative (Maurano et al., 2012), we only considered SNPs that have a dbSNP identifier and were found to be associated with a trait in at least two independent studies. 5,303 such SNP-trait or disease associations were used for the left and center panels of FIG. 14(A). 4,912 non-coding SNP-trait associations were used for FIG. 14(B), 15, and FIG. 20(C). 4,378 unique SNPs located outside coding regions were used for FIG. 14(A) right panel, and Table 20.

FIG. 14(A) right panel shows the distance distribution of trait-associated, non-coding SNPs to the nearest border of a region in the union of 86 enhancer sets. SNPs within these regions were assigned to the 0 bin.

Significance of the number of SNPs in super-enhancers was calculated using a permutation test. Super-enhancer-sized regions were randomly shifted on the chromosome of origin 10,000 times. The number of SNPs falling in these shifted regions was counted. No repetition resulted in the same or greater number of trait-associated SNPs in super-enhancer-sized regions.

Radar Plots

The density of trait-associated non-coding SNPs in super-enhancer domains and typical enhancers of individual cell and tissue samples were calculated by first counting the number of SNPs that are found in these regions (Table 20, sheets 3 and 4). The numbers were then divided by the number of base pairs super-enhancer domains and typical enhancers cover of the genome in these cells, and multiplied by 10 million, to give a SNP/10 MB dimension (FIG. 14(B), 5, FIG. 20(C)).

Selection of Oncogenes

Proto-oncogenes for display in FIG. 16(A) were selected based on their presence in the COSMIC (Catalogue Of Somatic Mutations In Cancer) or AOGIC (Amplified and Overexpressed Genes in Cancer) databases (Forbes et al., 2010; Santarius et al., 2010).

Forbes et al., Nucleic Acids Research, 2010; Santarius et al., Nat. Rev. Cancer, 2010

Cancer Hallmark Analysis

The following gene ontology categories were used as proxies for the characteristic hallmark capabilities that are thought to be acquired in cancers.

Angiogenesis:

-   -   GO:0001525—Angiogenesis

Enabling Replicative Immortality:

-   -   GO:0032200—Telomere organization     -   GO:0090398—Cellular senescence     -   GO:0090399—Replicative senescence

Activating Invasion:

-   -   GO:0034330—Cell junction organization     -   GO:0016477—Cell migration     -   GO:0010718—Positive regulation of epithelial to mesenchymal         transition     -   GO:0007155—Cell adhesion

Genome Instability:

-   -   GO:0006281—DNA repair     -   GO:0051383—Kinetochore organization     -   GO:0007065—Sister chromatid cohesion     -   GO:0000819—Sister chromatid segregation     -   GO:0051988—Regulation of attachment of spindle microtubules to         kinetochore     -   GO:0030997—Regulation of centriole-centriole cohesion     -   GO:0046605—Regulation of centrosome cycle     -   GO:0090224—Regulation of spindle organization     -   GO:0010695—Regulation of spindle pole body separation     -   GO:0031577—Spindle checkpoint

Resisting Cell Death:

-   -   GO:0060548—Negative regulation of cell death     -   GO:0012501—Programmed cell death     -   GO:0010941—Regulation of cell death

Disrupting Cellular Energetics:

-   -   GO:0006091—Generation of precursor metabolites and energy

Sustaining Proliferative Signaling:

-   -   GO:0007166—Cell surface receptor signaling pathway     -   GO:0070848—Response to growth factor stimulus

Tumor-Promoting Inflammation:

-   -   GO:0006954—Inflammatory response     -   GO:0045321—Leukocyte activation

Avoiding Immune Destruction:

-   -   GO:0002507—Tolerance induction     -   GO:0001910—Regulation of leukocyte mediated cytotoxicity     -   GO:0019882—Antigen processing and presentation     -   GO:0002767—Immune response-inhibiting cell surface receptor         signaling pathway

Evading Growth Suppressors:

-   -   GO:0007049—Cell cycle     -   GO:0008283—Cell proliferation

RNA-Seq

RNA extraction, purification, quality control and sequencing was performed as described (Sigova et al., 2013). Reads were aligned using TopHat (Trapnell et al., 2009) as a paired-end library with parameters -library-type fr-firststrand -microexon-search -coverage-search. RNA-Seq reads were not extended for density analyses, and reads that mapped to exonic sequences were removed for the analysis on FIG. 3-2C.

Gene Expression Analysis

Microarray gene expression data used on FIG. 18 were previously generated and described (Kagey et al., 2010; Example 1; Whyte et al., 2013).

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What is claimed is:
 1. A method of identifying a super enhancer, or functional fragment or variant thereof, in a cell, comprising: (a) identifying a genomic region of DNA within said cell characterized by a cluster of enhancers each of which bind a cognate transcription factor capable of interacting with Mediator to stimulate transcription of a target gene within said cell; (b) measuring in the identified genomic region a level of a super-enhancer component by evaluation of a surrogate mark of histone; and (c) identifying the genomic region as a super enhancer, or functional fragment or variant thereof, if the level of a surrogate mark of histone is greater than the level of a surrogate mark of histone occupying the average single enhancer. 